I would back up all the important files or stuff that would take forever to get back (skins in-game, customized in-game sounds, etc.), and re-install the OS if anything else starts happening.
I did that, and it took me a total of 30 mins to completly re-install the OS and all the drivers. After that, I scanned the saved files with several different anti-virus programs, and when I knew they were clean, I put them back where they were.
Re-installing a few games and putting your computer settings back to how you like is a lot simpler (and cheaper if you have to take it into a professional) than dealing with the headache of finding the damn thing, all the files its infected/screwed with, putting them back to rights, and then double-checking to make sure you didn't miss anything.