Backup, restoring, formatting info

Question

Some starting out information
I created this post to inform others of the various and essential ways to restore your machine, data, create backups and so forth.
10.6 and 10.7 are mostly covered with information current as of Oct 4, 2011 and subject to human error and change.
Only conduct any actions here if your prepared to take action on your own, the risk is yours, if not please seek assistance of qualified professional data recovery experts. Any product or site mention/link is purely for assistance purposes, doesn't represent a endorsement by me or Apple. Legalese blah.
Having many separate hardware copies
...of your data is essential, as the OS and programs can be replaced, but not your personal files (normally kept in your User folders of Music, Documents, Pictures, Sites, Movies etc.)
Apple currently doesn't supply much in the way of data recovery services, it's on YOU to make sure you have many copies of your personal data and perhaps many ways to restore your machine to a functional state.
There are three basic primary forms of backup and restore methods used on Macs, no one way is perfect, so a combination of ways may be better suited for your needs, but redundancy of methods and backups is the key.
1: TimeMachine Drive - which is a rotating in time image of your boot drive contents. If you remove something from your boot drive, eventually it will be removed from TimeMachine drive as well. TimeMachine drives cannot be booted from and can only restore. This is a very good basic option for most new to computers users as it's all automated (as long as the drive is connected) and gives "undelete" ability. It's not a complete solution and that's what the next two options are for.
Please, for your own sake if you don't have any backup plan or don't undestand geek speak, at least connect a new external drive and let automatic  TimeMachine popup do it's buisness.
From here on out everything TimeMachine, including restoring from a TM drive, I point you to our resident expert Pondini and his web page.
http://web.me.com/pondini/Time_Machine/Home.html
The steps here below out are a bit more advanced, but if you master them you will be in control of your computer and can save yourself.
2: Data / Storage Drives - these are drives that basically act as holders of data you wish to store, they don't do anything but hold your personal files in a permanent fashion unless you remove it. These are what one would use if their primary boot drive on their computer is getting full, since TimeMachine is a self rotating image, that can't be used for permanent or extra storage space. And clones are bootable images of the current boot drive, so they are subject to change as well. For all intensive purposes if you want to make sure your data doesn't disappear, to hold your personal data while your wiping your entire boot drive of all data and restoring OS X completely (aka "fresh install method"), then you use plain jane storage drives and maintain two separate hardware backups of your data at all times.
3: Hold the option key bootable Clone drive- these are (almost) exact images of your OS X partition and it's contents. The advantage with clones is in case your internal drive fails to boot, either for software or hardware reasons, you can boot from a clone, perform data recovery, drive repair and most of all get online, get help, and use your computer like almost nothing happened. In other words your life doesn't immediately stop to address a failed computer, you can in most cases continue working and resolve the issue later, or in the case of a software issue, just reverse clone form the latest clone image.
You can keep "states" of your OS X partition in a more permanent fashion unlike TimeMachine. For instance if your considering on upgrading to a new OS X version and not sure it will work, you can fall back onto the previous version of OS X at any time provided you made a clone first. Think of a clone as moving all your software to another piece of hardware and everything is almost exactly as it was before. Clones are the preferred method to upgrading to a new internal drive of perhaps larger capacity or speed.
Because of differences in computer hardware, you can't use a clone created on one Mac on another type of Mac. Only the same exact model can be perhaps be imaged to other Mac's. If your thinking this would be a nice way to pirate software, forget it. Each Mac has a ID associated with along with other identifying information.
Cloning software most Mac users use is Carbon Copy Cloner, (first and totally free, donations accepted) or Superduper (part free, part payware)
Drive size for clones: equal too or larger than the drive you intend to clone. If your going to upgrade the internal drive, then naturally one that matches or exceeds the new internal drive so you can use it as a clone afterwards. Best to clone to a larger drive than the original, as your data could exceed the smaller capacity drive.
Drive formatting 
Drive formatting is IMPORTANT and needs to be performed before a drive is used for the first time. Doesn't matter what it's used for a wrongly formatted drive can cause trouble later down the road if you don't understand drive maps and formatting. Apple's Disk Utility is the program used to format drives on a Mac, you can find it in the Applications/Utilities folder.
Partition Maps
These are roadmap instructions to how many partitions (separate areas on the physical drive) there are and what format they contain. Unfortunately not all operating systems can read others partition map schemes. So when one gets a NEW drive, it has to be completely erased and formatted to meet the partition map needs of the operating system and/or firmware used on the computer.
For instance Mac's need a GUID Partition Table (GPT), Windows uses a Master Boot Record (MBR), Linux uses either and reads anything.
Mac's can use a MBR as it can read some Windows drive formats, trouble is you won't be able to boot from any partition or drive with OS X on it without a GPT.
Since most drives come from the factory formatted MBR with a Fat32 (MSDOS) drive format, in order to use the drive on a Mac you need to format it GPT and OS X Extended (Journaled) (aka HFS+) in Apple's Disk Utility before using it.
If you place data on the drive and then realize it's the wrong partition map scheme and need to change it, then all the data off all the partitions on the entire drive must be removed first.
If you place data on a partition and you need to format it differently, you need to get the data off only that partition your going to reformat.
Current drive formats - there are many different formats how data is placed on the drive, and a drive can have many partitions each with a different format!
Windows currently uses:
NTFS  - used primarily for the operating system, but external drives can also be formatted this way
FAT32 (MSDOS in Apple's Disk Utility) this is a universal format between PC's and Macs, but limited to 4GB file sizes.
exFAT a new patented pending format both Mac's and PC's can currently read/write, it can have files in excesses of 4GB in size.
   (if you have Windows XP, a free exFAT download from Microsoft is available, just search for it)
Mac's OS X currently uses:
HFS+  (OS X Extended Journaled) required to boot OS X. All new Mac's come formatted this way, and perhaps some drive sold at Apple.
FAT32 (MSDOS) file exchange with PC's to 4GB sized files. Most drives sold in regular computer and office stores come formatted this way for PC's. (with a MBR)
exFAT - file exchange with PC's over 4GB sized files (Mac's pre 10.6.5 won't have exFAT)
Linux currently uses EXT4 for itself, can read/write anything.
Software called MacDrive installed on a Windows machine can read Apple's HFS formats.
Software like Tuxera, 3GNTFS, Paragon, allows Mac's to read the NTFS format of Windows drives.
It is PREFERRED not to rely upon third party software for reading drive formats, rather use a interchangeable format like FAT32 or exFAT instead.
When formatted a drive for both PC and Mac use, it's perhaps easier to format it on Windows into FAT32 or exFAT first, so you get the MBR, then confirm it works, then on the Mac before using it to transfer vital data over long distances.
Apple's Disk Utility allows one more partition to be carved out from the bottom clear existing OS X partition, you will learn all about this if you going the BootCamp route with Windows. I don't advise messing around unless you made backups of your data first.
When Bootcamp creates the Window partition it formats it MSDOS (FAT32) which you have to change to NTFS on the Windows installer disk before you can install Windows. Make sure you printout and read the Bootcamp instructions and have the Mac hardware drivers on hand.
If your machine keeps booting into Windows and gets stuck, simply hold the option key upon boot to select OS X and set OS X as the start up disk in System Preferences.
https://www.apple.com/support/bootcamp/
Restoring OS X 10.5 10.6. 10.7 - simple overwrite OS method
Ok, you got a OS X problem and you want to just reinstall OS X (and bundled Apple programs) without touching anything else, not your files or most third party programs.
1: Backup your user files via drag and drop methods of your User folders (Music, Documents, Pictures, Movies etc) regardless to a data drive as outlined above, as the problem you may be having could be more serious, like a hardware or firmware issue. Disconnect all other drives.
2: For Snow Leopard and Leopard - stick the original grey disk (free iLife included) into the computer and reboot holding down c, simply reinstall OS X (archive and install for Leopard)
If you upgraded Snow Leopard over Leopard, then your going to be using the white Snow Leopard Retail disks (no free iLife) and it naturally won't replace iLife, just OS X.
3: For Lion, you need a reliable, fast Internet connection. Hold Command r and boot into Lion Recovery, get online and simply reinstall Lion. You'll have to use the AppStore to download iLife.
4: Once you have done this and rebooted normally, immediately Software Update under the Apple Menu so your Apple programs match your files (like iPhoto Library and  iTunes Library that were changed with later versions)
5: Any programs you bought via App Store can be redownloaded by holding option key and clicking on Purchases.
Note: if you have installed root level system third party software, it may not function anymore, simply reinstall it from original sources.
Restoring OS X - 10.6  "fresh install method"
1: Backup your user files via drag and drop methods of your User folders (Music, Documents, Pictures, Movies etc) regardless to a data drive as outlined above, as the problem you may be having could be more serious, like a hardware or firmware issue. Disconnect all other drives.
2: Hold c and boot off the 10.6 grey disks (or if you want the free iLife on the 10.5 disks, then that first, then upgrade to 10.6) and use Disk Utility under the Utilities menu to erase the internal drive media.
Select media on left, click partition, click big box, select 1 partition, option GUID, format OS X Extended (journ) give it the same drive name as before, (to match pathnames used in your iTunes and other files to locate where music is stored on the drive) Format OS X Extended journaled click Apply and confirm.
Optional for privacy/security or for all new drives for better data retention. Select the drive, erase tab, erase>Security option Zero all data. Takes about a hour per 500GB.
3: When finished quit and install OS X Snow Leopard and reboot and see the familiar Welcome to Mac animation. (if you shutdown after installing, this makes a nice way to treat the new owner of your used Mac and lets then go through the setup process.)
4: When creating the new user, use the same user name as before, this again, like the same drive name, matches the pathnames in files to locate other files on your drive when you return your files. Use a different password naturally.
5: Next you install all your programs next, the more the better as they will run faster on hard drives if they are placed further near the front of the drive.
6: Lastly hook up your external data drive and move just the contents of your Music, Document, Pictures etc folders right back into their respective new folders on the new configuration.
Note: If you used this method to downgrade from Lion. It's possible your iPhoto and iTunes Library (and other Apple programs) may have altered their respective files. You need to be careful replacing the old copies with the newer altered versions. You can right or option click on iPhoto Library to "show package contents" to find the folder with the originals and re-import into the older iPhoto version format. For iTunes, the originals are in the folder, if you have  copy of the older iTunes Library files, then replace with those.  Ideally it's best to first make a Snow clone first BEFORE messing with Lion.
Note: Only a Mac that had Snow previously can be downgraded from Lion back to Snow, not a Mac that had Lion from the factory (some under certain circumstances)
Restoring OS X - 10.7 - wipe and install
1: Backup your user files via drag and drop methods of your User folders (Music, Documents, Pictures, Movies etc) regardless to a data drive as outlined above, as the problem you may be having could be more serious, like a hardware or firmware issue. Disconnect all other drives.
2: You have two options depending upon if your Mac had Snow Leopard previously. If it did, then you can go the above Restoring OS X - 10.6 "fresh install method" and then make a clone, then update to Lion via the AppStore with a very strong, reliable, fast Internet connection.
3: Your Mac came with OS X Lion, then you hold Command R and boot into Lion Recovery Partition, get online, use Disk Utility to Erase (and Zero if needed) the Lion OS X Partition, then quit and simply reinstall Lion from the menu.
Restoring OS X 10.7 (new drive, total reformat method)
1: Backup your user files via drag and drop methods of your User folders (Music, Documents, Pictures, Movies etc) regardless to a data drive as outlined above, as the problem you may be having could be more serious, like a hardware or firmware issue. Disconnect all other drives.
This method is for restoring Lion drive completely, including restoring a Lion Recovery Partition and reestablishing a GUID Partition Table (GPT) on the drive for machines that don't have Lion Internet Recovery. This could occur if the hard drive was replaced, the GPT got messed up, more than 2 multi-partition machines or whatever.
As you know Apple only allows one more partition to be created using Disk Utility, any more partitions on the drive require a complete GPT reformat.
2: You need to have a copy of your Lion Recovery Partition on a 1GB or larger USB stick created first using the Lion Recovery Disk Assistant software from Apple that copies YOUR PRESENT Lion Recovery Partition. So that means you need to have this made as soon as possible in advance or your going to have to buy the $69 Lion USB installer if you can't do the 10.6 to 10.7 upgrade method.
Lion Recovery Disk Assistant.
You must first FORMAT the USB GPT and OSX Extended (journ) in Disk Utility before using the Lion Recovery Disk Assistant.
https://support.apple.com/kb/dl1433
3: Stick the USB in, reboot the machine holding option key and get online, use Disk Utility to format the drive
Select media on left, click partition, click big box, select 1 partition, option GUID, format OS X Extended (journ) give it the same drive name as before, (to match pathnames used in your iTunes and other files to locate where music is stored on the drive)  Format OS X Extended journaled click Apply and confirm.
Optional for privacy/security or for all new drives for better data retention. Select the drive, erase tab, erase>Security option Zero all data. Takes about a hour per 500GB.
4: Formatting the drive like this will rebuilt the GPT if it was broken. Reinstall Lion from the menu and it will install Lion Recovery Partition and Lion at the same time.
If you have one of those new Mac's with Lion Internet Recovery, it's built into the firmware, so after a new drive install, rebooting should start the whole process automatically.
5: If you have a clone of OS X Lion previously made, then simply option boot from it and reverse clone it onto the OS X Lion Partition. When you clone 10.7 (and only 10.7) it just clones the OS X Lion Partition. Not the Lion Recovery Partition. That's why you need to reinstall the Lion Recovery Partition first (steps 1-4 above) then replace the Lion configuration with the previous cloned version.. You can choose to reverse clone the Lion Partition only, the machine will work without Lion Recovery Partition, but you may have need of it one day.
6: If you don't have a previous clone of your 10.7 OS X partition then when creating the new user, use the same user name as before, this again, like the same drive name as before, matches the pathnames in files iTunes uses to locate other files on your drive when you return your files. Use a different password naturally.
7: Next you install all your programs next, the more the better as they will run faster on hard drives if they are placed further near the front of the drive.
8: Lastly hook up your external data drive and move just the contents of your Music, Document, Pictures, Movies etc folders right back into their respective new folders on the new configuration.
Click on a picture to enlarge, drag and drop onto your desktop for keeping a copy, or use Command Shift 4 to take a picture.

Answer 1

Troubleshooting if a OS X reinstall is necessary
When one is considering a OS X reinstall, it usually means they can't find a specific cause for a issue or series of issues or instability and thereby think that just reinstalling everything will resolve the problem which it will most certainly could, but may not be required to expend that much effort. Not only that, it may not work in your case at all if your problem is in your very own files.
So starting from easiest to hardest you should try steps in this order, save yourself a lot of work and perhaps cure a minor issue quickly.
1: Disconnect backups, backup files if possible
Disconnect any auto-mated backup, including TimeMachine, auto-updating clones, auto-backup software during this period. If you haven't made a backup of your data (like Music, Documents, Pictures, Movies) now is a good time to do that to a external data / storage drive. Disconnect all drives/devices to prevent accidents or other issues from interfering with your judgement. Return to as close to "out of the box" as reasonably possible, with few wireless devices as possible. Always keep a wired mouse and keyboard handy.
1.5 Update your web browser plugins
Adobe Flash and Microsoft Silverlight epecially. For Lion only, Java is now a external plugin. Search "Apple support" for the Java plugin.
2: Perform a Safe Mode boot
Simply hold down the Shift Key while booting, this will disable kernel extension files that programs install upon booting and only use the ones Apple uses. This is especially effective when you boot a Mac and it results in a Grey Screen or "you must restart" (aka "Kernel Panic")
https://support.apple.com/kb/HT1455
What you do after this is update your third party programs (or uninstall them using their uninstaller to remove their kext file-s from your System/Library/Extensions folder) that have are perhaps causing your issues.
Problems with kext files usually occurs after a OS X Software Update, so if your in a mission critical environment, it's perhaps best to tread slowly and not update all your machines at one time.
3: Reset the SMC and PRAM
https://support.apple.com/kb/HT3964
https://support.apple.com/kb/HT1379
4: Grey Screen, Black/Blue Screen, Flashing question mark issues etc.
If you do a Google search:  apple support + [issue above] you can easily locate a support document Apple publishes themselves for you to read. Apple updates these support documents and sometimes discontinues some, some are old. Check the revision date to see if it pertains to your system. I could link to them, but because they change it's not as effective as doing the search and determining for yourself.
Ask for help on the forums, be detailed about your issue, the hardware you have, the operating system and the programs you use. We can't see your machine, we only know what you tell us.
5: Check with Disk Utility next
Run the following: In your Applications/Utilities folder Disk Utility > Repair Permissions (ignore the long list, things were changed permanently) also Verify Disk (if this gives a issue, it's a cause for concern, please mention it in the ASC forums for assistance).
If you have a issue after Verifying Disk, you need to (for 10.5 and 10.6 users) hold c and reboot off the 10.5/10.6 OS X installer disk and look for Disk Utilities and Run > Repair Disk (this can only be done while booted off another medium, why it's only "Verify Disk" before).
Once can also run Disk Utiliy > Reapir Permissions from the OS X install disk or Lion Recovery Partition as well if OS X won't boot.
If your on 10.7 Lion as there are no disks, hold command and r keys to boot into the Lion Recovery Partition and perform the same steps with Disk Utility on the OS X Lion Partition. (FYI: a partition is a separate area on the physical drive that appears to the computer to be another one, thus allowing multiple operating systems to be booted from the same drive.)
Hopefully that will resolve your issue, if not or even if it does, bring it to the forums for advice as it could be a sign of further trouble like a failing drive and you will need advice what to do next.
6: Check with OnyX
OnyX is a excellent part of the troubleshooting process, it's initial checks need to be performed and any warning in that regard brought to the forums for advice before proceeding any further.
Your next step is sort of a "nuke the site from orbit" approach by deleting all the computers cache files, which can become corrupt and cause instability. Since one really can't tell which one is causing the issue, the entire lot is allowed to be rebuilt in one massive stroke. So run ALL the cleaning and maintenance steps, you can cancel the in between reboots, but you MUST reboot when finished using OnyX or the cache files are not rebuilt. After rebooting your computer is going to act a little slow, but later return to optimum performance and hopefully your issue would have been resolved.
OnyX doesn't hurt your machine or files or programs, just allows the operating system to rebuild the cache files and perform maintenance tasks. It's not specifically a performance technique, although cleaning and resetting the caches with a reboot can increase the computers performance because whatever was causing the slowdown in the caches is now removed. You don't need to perform OnyX as part of any ritual or routine, OS X is pretty good at handling it's own maintenance.
OnyX also has the ability to check for corrupt preference files under the Verify tab. Corrupt .plist files problems exhibits themselves as programs failing to remember your settings or refusing to launch or hanging. Run the check to show only the corrupt ones and ask on the forums how to proceed to remove those .plist files usually in your Users/Library/Preferences folder (now hidden in Lion) but some are also located in System as well. So it's best to ask or you can use the free Easy Find to locate and delete the file, reboot and relaunch the program, the .plist file gets rebuilt. Again, be careful here as you can remove a essential system file if your not careful.
OnyX can be downloaded free from MacUpdate.com or visiting the Titanium Free developers site, be sure to use the version matched to your operating system version.
(Note: AppleJack is a another troubleshooting program, except it runs in Single User mode, aka a command line, has to be preinstalled ahead of time before problems occur. Benefit here is by holding Command S, you get to run it BEFORE the operating system loads. Works excellently for 10.5/10.6, but it hasn't been updated yet for Lion 10.7, although reports say everything works except the repair permissions portions. It can be found on MacUpdate.com and on Sourceforge.)
7: Create a new user account
2: Create a new user in the System Preferences > Accounts and log into it and use it for awhile, does your problem continue? If not, it means that your issue is localized to the other user account, if you can't find the problem/cure specifically, then consider copying the contents of (Music, Documents, Pictures, Movies, not Library) from the problem user account to the new user account via the ~/Users/Shared folder.
When your personal files are in the new user and you are using them there, does your problems return? If so, it's likely something wrong with your files themselves, which you will have to narrow down to the specific one.
8: Application reinstall
3: If your problem continues even in the other user and isn't a user file issue, then that usually means it's a something more global, works across multiple user account's. This could mean a bad program in the Applications folder, or one that starts it's self automatically (look in your log in items in System Preferences > Accounts)
Your next step would be to reinstall all your third party programs, the overwrite may clear the issue up. If you have purchased iLife separately (verses the free version that comes with a new Mac) , reinstall it from disk or redownload it from the AppStore by holding option key and clicking on Purchases. Overwriting the program doesn't overwrite your files, but may overwrite the settings you made in those programs. Also be sure to test the programs in both users.
Note: Some bundled Apple programs can be reinstalled by simply running the installer on the OS X disks that came with the computer. However some like PhotoBooth can only be resinstalled along with the entire OS, unless your willing to extract them manually using the program called Pacifist from CharlesSoft. You likely can avoid having to do that by following the next step.
9: Data recovery drive
If your at this stage, and before you stick that disk into the computer or hold command r to boot into Lion Recovery Partition, you likely need to consider making a "OS X Data Recovery Drive".
This is for those of you haven't managed to get a copy of your files off the computer yet. It can get very hairy after this point if you don't have a backup of your data. Basically your going to use a new external drive to format and install OS X onto, allowing you to hold option and boot off of it to attempt to get a copy of your files off first before doing anything.
So review the steps earlier and the pictures provided to do that first. Having your data safe is of the utmost importance, TimeMachine isn't always best course, have your files easily accessible on a normal storage drive so you can hook it up to any computer (Mac, Windows or Linux).
If you can't create or make a data recovery drive, don't have a backup of any kind, or not confident in proceeding PLEASE seek the assistance of qualified data recovery professionals as everything can be replaced except your data. A few hundred dollars (or even a few thousand for platter level dissection) is nothing compared to losing several thousand man hours of files, or songs or pictures you took on vacation.
10: OS X overwrite
What this does is overwrites the present OS X install with the version that is on the install disks or gotten via the Lion Recovery Partition. Again, make sure you have a copy of your data (Music, Doc's, Pictures and Movies) off the computer before proceeding or make a OS X Data Recovery Drive to assist you if OS X won't boot or run correctly to do it normally.
Key is to match the OS X version. 10.5 disks with installed 10.5, 10.6 disks with 10.6 installed, 10.7 Lion Recovery with 10.7 installed.  After using the disks, you need to immediately Software Update to get to the current version, unless the issue you are having occurred after a Software Update, then perhaps it's best to get online and ask questions before applying the updates.
OS X overwrites the installed version with the one you have, it doesn't touch your files or third party programs, and may or may not (depending upon what's on the disk) also overwrite your free iLife bundled on the disks.
Note that your going to perhaps get a older version of iLife than the one installed as it could have been updated via Software Update, so unless a Software update is causing your initial issue, you need to run Software Update immediately afterwards to update iLife (and other Apple bundled programs) to the current version.
The methods for OS X overwrite are mentioned in the above:
        Restoring OS X 10.5 10.6. 10.7 - simple overwrite OS method
11: OS X "fresh install"
The most drastic of all steps, this method first mandates that you have a copy of your files off the boot drive first (to a storage drive, not TimeMachine!), because everything is going bye bye. And the reason you don't want to depend upon TimeMachine is because whatever screwed up your machine has likely also screwed up TimeMachine, not mention the restore problems that occur (especially if your reverting to a earlier OS X version)
TimeMachine is a rotating image backup of your boot drive, it can become totally corrupt eventually from a prolonged issue or even malware as it deletes the old as it makes more recent copies of the new. Apple is always thinking forward and not considering your needs to perhaps revert to a earlier OS X version so restoring TM files to a earleir OS X version likely won't work all that well or won't be allowed. So TM isn't always the best solution for a fresh install. If you can TM restore and it works, by then all means do so, as it's a lot less work than a "fresh install". Use the easy method if you can, but keep your options open in case the hard method is the only way to get what you need done.
The object with a "fresh install" is your only going to save your user files (Music, Documents, Pictures, Movies) and the rest, including the operating system, programs etc. will be erased, the boot drive reformatted, the OS installed and updated, third party programs installed from fresh sources and finally (in case of malware a anti-virus scan on the backup files) returning the files back to the computer.
Instructions for 10.5/10.6 and 10.7 can be found above labeled
    Restoring OS X - 10.6  "fresh install method"
    Restoring OS X - 10.7 - wipe and install
The Restoring OS X 10.7 (new drive, total reformat method) is for the rare cases of a drive replacement, corrupt GPT or a major partition reformatting of the drive where all partitions, including the hidden Lion Recovery Partition, has to be rebuilt/replaced.