If you boot OS X with the Shift key held down, it'll start in safe mode and (among other things) run a repair on the startup volume as part of the boot process (note that you'll then want to reboot normally, because some things are disabled in safe mode).
Another option is to boot with Command-S held down, which starts in single-user mode (very minimal environment, just a full-screen command-line interface); you can then run
fsck -yf to repair the volume (note that fsck doesn't always fix everything on the first try, so if it repairs anything you should re-run it until it says the volume is ok).
Personally, I prefer the single-user option because it'll tell me about what it's repairing (safe boot just shows a progress thermometer, with no indication of what it's finding and/or fixing). For more details on both options, see Apple's KB article #TS1417.