From my standpoint as a "professional" (they pay me, I must know what I'm doing...

)
If a computer is really badly infected and it can be done, I'd rather re-image the machine and start from "scratch". That, of course, works better in larger corporate environments where you have a base image with most of the software already installed. (With software packaging for everything else)
When that isn't an option, there are some live-cd's out there that have Antivirus software included. (BartPE, Some linux live-cds) This way you have a known clean environment that can scan parts of the installed OS that you couldn't get to while its running. (or couldn't trust because it may be infected)