Have you tried running in Safe Mode to see if it will boot all the way? After the Macintosh chime, hold down Shift until it says it's going into Safe Mode. If you can get to the desktop, run Disk Utility and have it repair permissions.
As for running a repair on the drive, you might want either boot from the OS X discs and run a disk repair or you can boot into Single User Mode. Single User Mode will require you to type in some UNIX commands in order to run the disk fix, but you'll get the instructions on what do type before the command prompt (BTW, to get into this mode, hold down Apple-S after the Mac startup chime). Try using the discs first before going into this mode since it's much easier through the install discs.