It is a great idea actually. I run F-Prot with the updater from inside the mem key, and DrWebCureIt. Also removal tools downloaded from a clean source can work more when launched from inside the mem key, also Spyaudit, standalone scanning from Flash drives.
I think it is also good for rootkit scanning, but did not try that.
Make one yourself bootable disk drive: http://www.downloadsquad.com/2005/12/06/boot-windows-xp-off-a-usb-flash-drive/
What also could be a good idea is partition a USB partition as a Linux partiotion and scan from there the Windows environment.
I know you finally short circuit anything to everything, and that you will takethings into your own hands I have no single doubt about that. I know you. I have some ideas about this really, but we will discuss this in the future, you can bet, have to analyze the cd first.