OS X won't boot but Windows will

Hello, today I started having a serious problem with my iMac when booting it up. It won't get passed the apple logo with the spinning wheel, it just stays at this screen. I've times it at well over 20 minutes and it still refuses to start. I hae tried restarting while holding the commandoption+PR keys, I have also tried restarting after unplugging everything and leting it rest for a minute.
At one point I was able to get it to start after leaving it for about 5 minutes, but the computer ran very slowly upon startup. While it was running I tried doing a secure mepty trash because I've heard that might help a bit, and as it was emptying the trash other weird things started happening. My dock dissappeared for no reason at all, I got a message saying something about a conflict with fonts and that they had been moved around or something, then the computer pretty much locked up, not even letting me quit applications or select anything.
I should note that interestingly enough, my windows boot camp partition is functioning normally and fine, and the problems on the mac side seem to have come out of no where. Although I have noticed that upon booting up into the mac side, before the spinning wheel appears, there is a grey status bar that appears where the spinning wheel should be, beneath the apple logo.
I am at a loss for what I should do at this point as nothing seems to be working. Any ideas?

This usually means critical system files are damaged. Try the following:
How to Perform an Archive and Install
An Archive and Install will NOT erase your hard drive, but you must have sufficient free space for a second OS X installation which could be from 3-9 GBs depending upon the version of OS X and selected installation options. The free space requirement is over and above normal free space requirements which should be at least 6-10 GBs. Read all the linked references carefully before proceeding.
1. Be sure to use Disk Utility first to repair the disk before performing the Archive and Install.
Repairing the Hard Drive and Permissions
Boot from your OS X 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 Installer menu (Utilities menu for Tiger, Leopard or Snow Leopard.) 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. Now restart normally.
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.
2. Do not proceed with an Archive and Install if DU reports errors it cannot fix. In that case use Disk Warrior and/or TechTool Pro to repair the hard drive. If neither can repair the drive, then you will have to erase the drive and reinstall from scratch.
3. Boot from your OS X Installer disc. After the installer loads select your language and click on the Continue button. When you reach the screen to select a destination drive click once on the destination drive then click on the Option button. Select the Archive and Install option. You have an option to preserve users and network preferences. Only select this option if you are sure you have no corrupted files in your user accounts. Otherwise leave this option unchecked. Click on the OK button and continue with the OS X Installation.
4. Upon completion of the Archive and Install you will have a Previous System Folder in the root directory. You should retain the PSF until you are sure you do not need to manually transfer any items from the PSF to your newly installed system.
5. After moving any items you want to keep from the PSF you should delete it. You can back it up if you prefer, but you must delete it from the hard drive.
6. You can now download a Combo Updater directly from Apple's download site to update your new system to the desired version as well as install any security or other updates. You can also do this using Software Update.

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    Microsoft cannot make any representations regarding the quality, safety, or suitability of any software or information found there. There are inherent dangers in the use of any software found on the Internet, and Microsoft cautions you to make sure that you
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    Fixes and diagnostic:
    1. Diagnostic lights on mother board cycle and and say OK.
    2. I can get to Win98 Safe-Mode or Command prompt.
    2. I don't have any other PCI cards installed except video.
    3. I'm using only one of the memory sticks just to rule out the other (tried both).
    4.  I have most of the on-board peripherals disabled (sound, ethernet, serial. parallel, etc...).
    5. Tried upping the voltage on memory. Same problem.
    6. Tried setting memory for 100mhz. Same problem.
    7. Tried reseating the memory. Same problem.
    8. CPU temp is well within range at around 109F.
    Questions:
    What could the problem possibly be? I will try anything!
    1. Is there some kind of safe mode for the hard drive settings?
    2. Is there some kind of safe mode for memory speed?
    3. Give me some hints! Upgrading the MB shouldn't be this hard! What am I overlooking? Thanks for any replies!

    Quote
    Originally posted by Falconis Progmadn
    This can easily be caused by not setting the jumper pins correctly when having both of the HDDs installed on the same IDE cable.
    Obviously you would have to change the jumper short every time you retry each HDD.
    I am not following your line of thinking here. Win98 needs to on the primary drive, primary channel in most cases, yet XP can boot from any location, and any drive letter. So why would there be a need to constantly swap jumpers? Only thing needed is the Boot.ini file on the main drive, and it will boot from any OS listed there.

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