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GMER does more than remove rootkits. One feature I really like: in the Processes tab, press "Kill All", this leaves the absolute minimum of processes running - even fewer than Windows Safe Mode.

Then go to the bottom of the window, there's a field labeled "Command", press the "..." button next to it, browse to an AV/malware scanner, select it, then press the "Run" button.

This lets you run a scan that's even better than scanning in Safe Mode - and it's faster than rebooting into Safe Mode. It doesn't work with all scanners, though.