I don't know if anyone knew about this before and I'm just late to the game, but Microsoft has an ActiveX-based system scanner. It basically scours your OS install for things that are out of place and could be tampered. It's free and it's not bad. It requires Internet Explorer (not sure which version, I'm using IE8) and Windows (obviously). Check it out at
http://onecare.live.com/site/en-us/default.htm.