Hi there,
You should not try to Repair Permissiond any more until the Disk is fixed. Hopefully you have a backup.
"Try Disk Utility
1. Insert the Mac OS X Install disc that came with your computer, then restart the computer while holding the C key.
2. When your computer finishes starting up from the disc, choose Disk Utility from the Installer menu. (In Mac OS X 10.4 or later, you must select your language first.)
Important: Do not click Continue in the first screen of the Installer. If you do, you must restart from the disc again to access Disk Utility.
3. Click the First Aid tab.
4. Click the disclosure triangle to the left of the hard drive icon to display the names of your hard disk volumes and partitions.
5. Select your Mac OS X volume.
6. Click Repair. Disk Utility checks and repairs the disk."
http://docs.info.apple.com/article.html?artnum=106214
Then Safe Boot from the HD, (holding Shift key down at bootup), run Disk Utility in Applications>Utilities, then highlight your drive, click on Repair Permissions, reboot when it finishes.
You should quit using the computer asap. Possibility exists of losing everything. Backup if at all possible.
Unfortunately DU can't fix all that much, your best bet is DiskWarrior, you need the CD though.
http://www.alsoft.com/DiskWarrior/