I recently built a computer that's running on 64 bit Windows Vista. The boot drive is a 160 gig Seagate ATA100 drive, which has never given me problems. I have 2 1TB hard drives and 2 DVD drives, all SATA, all of which occasionally 'disappear.' They either don't show up as the computer is booting, or more commonly simply stop working randomly after windows is running. They don't necessarily disappear all at once, usually just one or another of them stops being recognized, causing a crash if I happen to be accessing data from a particular drive when it decides to stop working. I can't find any pattern to the problem, it seems totally random.

If they aren't showing up during POST, I would suspect a motherboard problem like a flaky controller or perhaps a power supply problem. Unhook as many drives as possible and connect to different power supply rails and see if issue changes.