I was hit by Vundo a while back, and usually when I get something tough, I reinstall windows... Using the "leave everything intact, delete windows, and reinstall it to the same folder" option. It survived that (about the only one I've seen do that).
So I ran combofix and that killed it on the spot.
I've never had a problem with rootkits, that I know of, but I've also gotten pretty adept at avoiding stuff online, so considering I do occasionally browse warez sites and such, when the need arises, I've managed to keep my system a lot cleaner than it has any right to have been.