For REALLY resistant problems, those that just don't get fixed by tools for the purpose and are too persistent to kill off manually, darik's boot and nuke.
Bear in mind that this is a program that runs off a boot disk and without confirmation, sterilizes the hard drive with a multi-pass overwrite. It will delete EVERYTHING, not just the virus/malware.
Unsure if it will delete hypervisor-level rootkits though.