SysInternals, famous for all its good tools for Windows systems (Process Explorer is one of my favourite) today is out with a new free security tool called RootkitRevealer.
RootkitRevealer is an advanced root kit detection utility that runs on Windows NT 4 and higher and its output lists Registry and file system API discrepancies that may indicate the presence of a user-mode or kernel-mode rootkit (a "rootkit" is a technique used by malware, including viruses, spyware, and trojans, to hide their presence from spyware blockers, antivirus, and system management utilities).
This tools has a GUI version (really useful) and a command-line version, and you can download it from HERE. Great work SysInternals (as usual)! 