Check out my other various ergonomic Instructables:
Stand Up Desk, Standing Desk, How to make a vertical, ergonomic (tie-fighter) keyboard, and Create an Ergonomic Standing Desk and Office on the Go.
Step 1: Research, Experiment, and Listen
This project documents what I have done to control my RSI. Controlling yours will be different and you will need to research, experiment, and listen to your body.
Resources I found useful: "Repetitive Strain Injury : A Computer User's Guide" by Emil Pascarelli and Deborah Quilter. Both authors have new books that are probably also good. Hand University has great pictures of the wrist to help you understand what might be inflamed. The ATIC Lab at MIT has resources and also allows students to borrow various keyboards and pointing devices to try them out, which is truly invaluable.
For me, the hardest part of this process was listening to my body. The pain usually does not come immediately, so it is often very difficult to determine what activity caused it. What I found is that pain is not discrete. There are levels of feeling before true pain that can signal distress or damage. Generally, these manifest themselves as "being aware" of some part of your body. For example, after typing on a small or badly positioned keyboard I will become aware of my wrists; I try to recognize these signals and take a break or stop to prevent progressing into pain.
Step 2: Take Frequent Breaks
I use Workrave to help remind me to pause. It has multiple timers that are only active when you are mousing and typing and can be set to actually prevent you from overusing your computer, if you desire.
I have a micro-pause of 45 seconds for every 3 minutes of typing/mousing, and a 10 minute rest-break for every 30 minutes when I stretch, walk around, and do non-computer-related work. This may seem maddening, but it works for me. The frequent micro-pauses are not even lost time; while pausing, I think about the next thing I am going to write or do and can do it quickly and directly when the pause is over. They also come with plenty of warning, so I can scroll to the next page of a document and continue reading with my hands at rest.
Although it may seem like you are pulse-width modulating your work with breaks, I have found my productivity equal or better than before I took breaks. With your computer telling you to take breaks, you can get angry at it and not at your hands when they force you to stop.
Now that I work primarily on a Mac, I've been using AntiRSI. It doesn't have the same level of control as Workrave (30 second micro pauses are the max!), but accomplishes nearly the same goal.
Step 3: Stretch
I hold each of these for 30 seconds or longer. With one hand straight out in front of me and my fingers pointed down, I pull my fingers towards my body to stretch the inside of my forearms. Next, I put my arms out from my sides, make fists, and bend my wrists downwards to stretch the outside of my forearms. Occasionally, with the backside of my hands, I push against something solid to get an even deeper stretch. With my fingers pointed away from me, I twist my hands at the wrist around my forearms once in each direction. I finish up by hanging from a pull-up bar or something similar for 30 seconds with straight arms and 30 seconds with my arms bent -- this part often feels great as my weight pulls straight through my wrists.
Step 4: Position Your Arms
To dial in the proper height, I use under-desk keyboard drawers such as the Kensington 60044 and 3M AKT200SL. On both of these models, I've removed the gel-filled wrist rests so that my keyboard fits properly. An important feature is that the mouse platform is independent of the keyboard platform. It is unlikely that your keyboard and mouse will be perfectly positioned for you at the same level or angle. I prefer the Kensington because it is continuously adjustable while the 3M has detents.
After taking breaks, I consider arm position the most important thing. When I'm forced to use a laptop, I put the computer in my lap and make sure not to rest my arms on it while typing.
Step 5: Choice of Keyboard and Mouse
I decided on a Goldtouch keyboard and 3M Ergonomic mouse. I felt that many of my problems stemmed from rotating my hands from a neutral, handshake-like position to a flat, fingers down position to type and mouse. This keyboard and mouse lets me work in a position closer to neutral.
These devices are not perfect. Previously, I used a Microsoft split keyboard and a Logitech trackball (Logitech Cordless Trackman FX Optical Trackball, which appears to be discontinued). Something that works for you now may not work in a year. My thinking on this is blunt: Each device overuses and destroys a different set of tendons and muscles, and to keep working, you may have to cycle through which set is currently being wrecked while another heals.
Step 6: Use Two Mice at Once
I just picked up a Wireless Right Handed Vertical Mouse Version 3 and tried to use it in combination with my Version 2 Left Handed mouse. While the two mice still work together, they are different! The buttons have been changed between versions: version 2 has its right-click button in the center, while version 3 has it on the bottom of the stack of buttons! Also, the resolutions of the mice are different, so moving the left mouse causes less cursor movement than moving the right mouse. Since my computer doesn't know I'm using two mice, there's no way to compensate! Though, I've sorted out the button issue by using USB OverDrive to map both second and third buttons to "right click." If you plan to use two mice, make sure they are the resolution and button layout.
Step 7: Position Your Screen
I built special stands for my laptop and monitor. As an aside, using two monitors is great; your eye can more easily refocus on something new when you look in a different spot then when you flash open another program window, and there's no key-strokes involved.
Step 8: Sit Up Straight But Move Around
I used to use a kneel chair but decided I didn't want the constant pressure on my knees.
Step 9: Manage Pain
Some people swear by Ibuprofen for its anti-inflammatory capabilities. Personally, I am weary of taking a pain-killer because it may allow me to ignore the pain and truly damage myself. See what works for you.
I have been experimenting with curcuminoids, which are found in turmeric. They have anti-inflammatory effects, but no pain-killing. Jury is still out!
UPDATE - The curcuminoids had no effect. However, what has been remarkably useful is fish oil capsules. EPA, one of the omega-3 fatty acids found in fish oil, acts as an anti-inflammatory. 2000 mg of fish oil twice a day makes my wrists feel normal even after a full day of typing. Though, I can still overdo it: My stretch break program was inadvertently turned off for half a day and I hurt afterwards. Lots of people are now recommending fish oil for overall good health, so there's no harm in giving it a try.
Step 10: Improve
Don't be embarrassed by your crazy-looking setup. People will make fun of you, but that's easier to take than the pain.
Step 11: Other Factors and Ancedotes
I once had an RSI flare-up after using the stupid track-point on my laptop for 3 hours straight in a boring meeting. A tendon that controls my thumb or first finger became so seriously inflamed that the pressure required to pick up a pen with my thumb and first finger was enough to bring tears to my eyes. However, it was was the frustration of having a useless hand that would make me cry out.
I swore off computers for three weeks. My loving wife typed the few email responses that were actually critical or couldn't be done with a phone call. Luckily, the third week coincided with a kitesurfing vacation. After a full week on the water, the tendon healed. Since implementing all of these techniques, it hasn't bothered me since (other tendons still give me problems, but not nearly as severe).
I went to physical therapy for a while and decided it was a mixed bag. The ultrasound and massages were not really helping me. However, they did determine that my wrists and fingers are hypermobile, which is why some of the standard RSI stretches were not working for me.
As an experiment, I gave up cycling to work and took the bus. Without the exercise and relaxation of biking, my wrists felt much worse. They promptly improved once I started biking again.