Microsoft has a beta tool out that will allow you to remove rootkits and other malware. It's buried in their site and not promoted at all. Judging from the language used it's a tool recommended by Microsoft Support when customers have a really messed up system. However it looks like a useful addition to the average IT guy's arsenal. I've seen some pretty badly compromised systems recently and normally I just nuke the entire OS and start over, but there are cases where removal of the problem malware would be a real time saver.
They have 2 ISO images available; 32-bit and 64-bit. I'll be adding these CDs to my collection.Microsoft Standalone System Sweeper Beta