One of my co-workers swears by using a track-ball for Q3 style games...I myself could not get used to one. My set-up is as follows:

W = Forward
S = Back (I use the mouse and W&S to move side to side, not easy using A&D to move side to side)
MS Intellimouse Explorer mouse with the wheel set up to scroll thru the weapons. Space bar to jump, C to crouch. Thats it.