I started working a lot on the computer a few years ago and started getting neck pain, wrist pain, etc. Here are the solutions that worked for me:
1. Cloth mousepad: Easier on your arm. I actually use a big one from Xtrac. The larger size helps because you don't have to constantly move your mouse back to keep it centered.
2. Ergonomic keyboard: I have a wireless ergonomic keyboard from Microsoft. It took awhile to get the hang of, but I absolutely love it now. I've done a lot of tape transcription work over the last few years (from microcassette voice to Word) and it's really helped my wrists not to hurt.
3. Chair/posture: Before I had a curved "slacker" chair that I really liked, but after spending 8 hours+ on the computer, I knew I had to get something else. I found a nice "task chair" from Staples for $99 made out of cloth (fabric instead of leather). The back is straight up and that really helped my back pain. Also, you need good posture, because you can slouch in any chair. Sitting up straight helped alleviate my neck pain. It's hard to sit up straight at first, but a little trick I learned is to scoot your rear all the way back into the chair, which makes the rest of your body kind of sit up automatically. Takes a while to break the slouching habit.
4. Monitor position: I also found that where the monitor is placed makes a big deal. I was always looking down to the monitor, which also gave me neck pain. I think they recommend that your eyes are level with 25% down from the top of the screen. I found that the best for me is to have the screen slightly angled towards me and looking near the top at eye level.
I spend about 12 hours a day now on a computer (between work and school) and I have no pain to speak anymore. Like jesusfr3ak4evr said, the important thing is to do what's comfortable for you. Not all ergonomic advice is necessarily good advice for your particular body and situation. Anyway, that's what's worked for me.