I usually boot into a live CD and clean what I can manually, then follow up with a virus scan + Hitman Pro and Malwarebytes. Hitman is kicking some serious butt!
back to topic i use combo fix, portable sas, avg rescue cd, mbam, hijack this and process explorer. When it comes to nuke and pave i do it if the computer is completely infested and is basically already crippled but if its a so so infection i do manual since the costumers like having their data and not getting it wiped out.