[AgentZero]

Had a similar problem about six months back as well. Everything looked ok, but the system ran horribly slow. I did every virus/spyware scan I could think of, looked through the BIOS, and there was absolutely nothing that indicated the machine should be running abnormally. In the end, I backed up my important stuff, formatted the HD and reinstalled Windows.

Which was fun.

I highly recommend Fyron's suggestion of making a separate Windows partition, since then you don't have to worry so much about backups, especially with big stuff like video & music files.