I narrowed it down to 2 causes:
1: My car has a manual transmission, and all that gear changing in my commute irritates the nerves.
2: Mousing. I spend a lot of time using the mouse to move all those damned windows around. I switched to using my left hand for the mouse. Now the only times my right wrist hurts are driving for extended periods in slow traffic, or using the touchpad on my laptop a lot (I still use my right hand by habit).
Switching to Dvorak might be the most obvious way to reduce RSI, but I don't think it is the one best thing you can do.
Another thing I'm doing to combat #2 above is trying to get as much of my programming done in Emacs as possible. I also have, "learn a decent window manager" on my list of things to do.
Once I can do all programming & code browsing/navigation in Emacs, and also use the keyboard to manage my windows... maybe Dvorak would help me.