This article on PC posture is worth the read. I occassionally suffer wrist pain and eye strain from working in front of a computer all day. I first thought it was because of something I did, maybe I pulled a muscle playing ultimate or working out. Nope. My arm rests, keyboard, and mouse pad were in the wrong place. It puts strain on my mousing wrist because I had to constantly bend it at odd angles. So I reorganized my desk and bought some better ergonomic stuff. No more pain.
I also have found that if I keep any desktop setup for too long it will create problems. I try to make slight changes on a regular basis just to keep everything fresh and prevent any sort of repetitive motion problems.