Couldn't find this anywhere on the site so I thought that I would share the link with you guys :

Strider GhostBuster Rootkit Detection

Simple explanation on how it works :

Bruce Schneier

Here's how it works: The user has the GhostBuster program on a CD. He sticks the CD in the drive, and from within the (possibly corrupted) OS, the checker program runs: stopping all other user programs, flushing the caches, and then doing a complete checksum of all files on the disk and a scan of any registry keys that could autostart the system, writing out the results to a file on the hard drive.

Then the user is instructed to press the reset button, the CD boots its own OS, and the scan is repeated. Any differences indicate a rootkit or other stealth software, without the need for knowing what particular rootkits are or the proper checksums for the programs installed on disk.

Simple. Clever. Elegant.
Why doesn't MS include programs like this is their OS ?