If you are sure that you have a good system(includes virus free, etc.) presently, manually create a system Restore point. Reboot. Then go to disk cleanup to remove all system restore points but the most recent one.
Back in 2005 (and again in 2006) my Windows XP crashed on me and I went through system restore. Now I have about 10 gigs of space taken up that I don't use, but I can't delete the files.
And, to top that off, I can't even see about half the files. They just...aren't there. (it says there's 3 gigs of space taken up, but no files)