Something that has worked well for me is to take the hard drive out and put it in a USB case, then plug it into a healthy computer and scan it from there as an external drive. You don't even really need to remove the drive, you just need to expose it enough to get an IDE/SATA cable from it to an opened up usb drive enclosure - you can even leave the power plugged in and use the infected computer to power it (although you'll need to unplug the power lead while you swap the data leads).
Because it's treated purely as a data drive nothing on it executes, so anything nasty lurking on there doesn't get a chance to (a) infect you or (b) hide itself from your anti-virus software.
That's the way we used to do it when I was in the IT office ...
Gary
ps - watch out for System Restore Points - described by one of the top geeks I know as "Microsoft's way of ensuring that you can never really get rid of a virus"

Gary