OSX 10.6.8 hangs: troubleshooting tips?

Question

Hello All
Using a MacPro1,1 Dual-Core Intel Xeon, 7 Gb ram and plenty hard disk space.
My Mac recently started to hang. I have the beach ball appearing randomly and computer freezes for a number of seconds.
It is not like a rogue process is hogging all the CPU power (on activity monitor, the CPU usage goes down to zero when my mac hangs).
I have done a disk + permission check and repair.
Computer works fine in Safe boot mode.
I was told that this is probably something to do either with the system preferences or with an apps that launches at start, possibly amongst the most recently installed ones.
Question: what would be a safe way to find the fault? I am trying to avoid a reinstall here.
Is it like in the olden days where you fault-find by removing half of your extensions and put them in a folder on your desktop (in that case, i understand that would be the .plist from the system) and try and slowly isolate the faulty extension? Anything i can find via the console or the Activity Monitor?
Any input would be welcome.
Thanks

Answer 1

First, visit The XLab FAQs and read the FAQ on the SBBOD issue. Next, restart into Safe Mode and do the following:
Repair the Hard Drive and Permissions
Boot from your Snow Leopard Installer disc. After the installer loads select your language and click on the Continue button. When the menu bar appears select Disk Utility from the Utilities menu. After DU loads select your hard drive entry (mfgr.'s ID and drive size) from the the left side list.  In the DU status area you will see an entry for the S.M.A.R.T. status of the hard drive.  If it does not say "Verified" then the hard drive is failing or failed. (SMART status is not reported on external Firewire or USB drives.) If the drive is "Verified" then select your OS X volume from the list on the left (sub-entry below the drive entry,) click on the First Aid tab, then click on the Repair Disk button. If DU reports any errors that have been fixed, then re-run Repair Disk until no errors are reported. If no errors are reported click on the Repair Permissions button. Wait until the operation completes, then quit DU and return to the installer.
If DU reports errors it cannot fix, then you will need Disk Warrior and/or Tech Tool Pro to repair the drive. If you don't have either of them or if neither of them can fix the drive, then you will need to reformat the drive and reinstall OS X.
Now restart normally. If this has not helped then read the following:
Kappy's Personal Suggestions for OS X Maintenance
For disk repairs use Disk Utility.  For situations DU cannot handle the best third-party utilities are: Disk Warrior;  DW only fixes problems with the disk directory, but most disk problems are caused by directory corruption; Disk Warrior 4.x is now Intel Mac compatible. Drive Genius provides additional tools not found in Disk Warrior.  Versions 1.5.1 and later are Intel Mac compatible.
OS X performs certain maintenance functions that are scheduled to occur on a daily, weekly, or monthly period. The maintenance scripts run in the early AM only if the computer is turned on 24/7 (no sleep.) If this isn't the case, then an excellent solution is to download and install a shareware utility such as Macaroni, JAW PseudoAnacron, or Anacron that will automate the maintenance activity regardless of whether the computer is turned off or asleep.  Dependence upon third-party utilities to run the periodic maintenance scripts was significantly reduced since Tiger.  These utilities have limited or no functionality with Snow Leopard or Lion and should not be installed.
OS X automatically defragments files less than 20 MBs in size, so unless you have a disk full of very large files there's little need for defragmenting the hard drive. As for virus protection there are few if any such animals affecting OS X. You can protect the computer easily using the freeware Open Source virus protection software ClamXAV. Personally I would avoid most commercial anti-virus software because of their potential for causing problems. For more about malware see Macintosh Virus Guide.
I would also recommend downloading a utility such as TinkerTool System, OnyX 2.4.3, or Cocktail 5.1.1 that you can use for periodic maintenance such as removing old log files and archives, clearing caches, etc.
For emergency repairs install the freeware utility Applejack.  If you cannot start up in OS X, you may be able to start in single-user mode from which you can run Applejack to do a whole set of repair and maintenance routines from the command line.  Note that AppleJack 1.5 is required for Leopard. AppleJack 1.6 is compatible with Snow Leopard. There is no confirmation that this version also works with Lion.
When you install any new system software or updates be sure to repair the hard drive and permissions beforehand. I also recommend booting into safe mode before doing system software updates.
Get an external Firewire drive at least equal in size to the internal hard drive and make (and maintain) a bootable clone/backup. You can make a bootable clone using the Restore option of Disk Utility. You can also make and maintain clones with good backup software. My personal recommendations are (order is not significant):
Carbon Copy Cloner
Data Backup
Deja Vu
SuperDuper!
SyncTwoFolders
Synk Pro
Synk Standard
Tri-Backup
Visit The XLab FAQs and read the FAQs on maintenance, optimization, virus protection, and backup and restore.
Additional suggestions will be found in Mac Maintenance Quick Assist.
Referenced software can be found at CNet Downloads or MacUpdate.
Be sure you have an adequate amount of RAM installed for the number of applications you run concurrently. Be sure you leave a minimum of 10% of the hard drive's capacity as free space.