As a geek, I've been known to sit in front of a computer for 12 hours at a stretch, or more, barely getting up for food and restroom. As you can imagine, this means that ergonomics is very important to me; and I've learned the hard way, the costs of not having things set up well.
One of the most basic lessons I learned is about my positioning. It is amazing what a difference a good chair and desk layout can make. Your chair should adjust so your upper legs are parallel with the floor, and your arms resting naturally should extend parallel to the floor to access the keyboard and mouse. I prefer a low desk (and a corner arrangement) and an armless chair, that allows my arms to rest on the desk. But for some, a low desk and a chair with adjustable armrests work well.
Those little keyboard trays that sit under desks can save space, but it can be tricky to adjust the arms on your chair for proper arrangement. Usually your arms are sloping up or down, causing blood to rush from your hands or into them; both are not optimum. And a mouse should generally be on the same surface (and level) as the keyboard and easy to reach; which is often impossible with those trays. So if you work a lot on your computer, or want to aid your comfort, I'd recommend getting rid of under-desk trays and using your desk's surface.
For some, mice can irritate repetitive stress injuries; for many, a trackball or trackpad can. I find the latter two cause me far more problems; but generally, if your body is getting sore using one, then changing to a different input device can help, if for no other reason that the change will give you a chance to recover.
If you are typing a lot, and getting symptoms of carpal tunnel syndrome or one of the similar or related tortures (usually noticed by pain, tingling, or numbness in the fingers, often on the outside of the hand; or pain in the wrist); then changing the keyboard style, or going to voice input, can be a big help. I find that voice dictation system is much too slow, inaccurate and just annoying to use; but they are better than nothing. The alternate keyboards, with split keyboard arrangements, and tilt, can be a big help. They also have the side benefit of helping to force people to touch type; which can help as well. Generally, if you don't touch type then learn; this will be an excellent investment in your health and productivity.
Displays (monitors) should be set up so that your eye level is about 2/3rds of the way up the screen. This prevents neck fatigue, from looking down (or up) all day. And facing a wall is better than facing a window or out of the office. The reason is that eyestrain often comes from focusing in close, and far away a lot; causing the muscles of the eyes changing your depth of view. Not to mention the strain of two different light levels.
Also, monitors are important. Having higher resolution monitors are a good idea. Not because you should bump them to their maximum size, and view text very tiny, but because those monitors have a higher refresh rate. This is how many times per second (Hz) the entire display will refresh itself. The faster that happens, generally the sharper the image appears and the less stressful on the eye things are.
Another overlooked thing is that people are more productive when they have a quiet (non-chaotic) place to work. I'm not saying that you can't listen to music or be in the thick of things; just know that noisy, chaotic workplaces generally distract people, reduce productivity, and cause stress.
Laptops have keyboards in uncomfortable positions, displays that make you look down at them, and wonky little pointing devices, all that may allow them to be portable, but make them pure torture when it comes to good ergonomics. If you use a laptop, consider hooking it up to an external monitor and keyboard in your primary workplace, or "dock it"; so that you can arrange things much better. If you try it that way for a while, I'm sure you'll be glad you did.
So have fun setting up your new workspace, and hope it helps you become the power-working nerd that you always wanted to be.