McAfee Avert Labs has released a standalone, free program called Rootkit Detective. It scans a PC and reports hidden files, registry entries, and processes.
I tried it, it seems to do what they say. So, cool.
Like other programs aimed at rootkits (e.g. HJT), the program makes no judgements with regard to what's legit and what isn't. That's for the user to determine (McAfee stresses that this program is for experienced persons to use only).
Check it out here: McAfee Threat Center: Root Kit Detective