In your situation, I know exactly what I'd do...but you probably won't like the answer.
Format and redo the partition.
Hopefully you have another computer you'd be able to use to back up the important things, or a second hard drive...or something.
I would seriously consider this option. Continued use of a drive that is having such problems can cause everything to just...well, get worse. I don't know if it could actually lead to hardware problems concerning your hard drive...but I'd think that it could.
If you do choose this option, a suggestion for you...if you're not using the NTFS file system, use it. It will save you problems like this in the future. And if you're already using it? *shrug* Consider Linux. ^_^