As
JellyBaby stated, make sure you're using OpenGL for Win2000. Direct3D has some problems in Windows 2000, especially in Counterstrike. A friend of mine just purchased a CL GF2 Ultra, and he runs Win2000. Opened up Counterstrike, and the frames where a nice whack in the head.

I voted Win98SE, obviously, since I'm a CS junkie.
Win98SE / Win2000 or Whistler Beta 1 / Slackware Linux - Triple boot is the best way to go.
G|T