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I like using Avast with MalwareBytes.
On so may systems that I have worked on, I will open up Avast's real time file monitor and then start up MalwareBytes and then watch the files click away. One more than one occasion, as the malware scan is going down the folder hierarchy Avast will detect a bad file as a nasty file tries to write itself to a location that has already been scanned.

You also can't forget about rkill. It's small and quick killing all questionable process so you will be able to install and run your anti-virus and anti-malware on badly infected machines.
http://www.bleepingcomputer.com/download/rkill/