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.