Bill Clementson mentioned recently in his blog different methods of making sure one's wrists "survives emacs". He missed one method, though probably from the fact that it seems completely counter-intuitive. Saying that, it has seen me use emacs on a more-or-less daily basis for the last 14-or-so years. The method? "Go beyond touch-typing" My normal finger positioning (once trained in typewriter class, to the point where I could type reasonably fast with a screen between me and the keyboard) is fairly fluid, with my right (stronger) hand usually pressing two keys for each my left presses. It has some curious draw-backs, I am more likely to transpose characters, especially when they alternate between fingers and I do need to re-sync hands and keyboard at regular intervals. I also need to not have my hands, wrists or arms resting on anything. Apart from that, I use either a SE/FI keyboard layout (at home) or a UK layout (at work), with no swapping of Control or CapsLock (though when typing in X at home, CapsLock is disabled completely).
Part of it is, as mentioned there, choosing a good keyboard. My keyboard of choice is a buckle-spring keyboard, they make a bit of a racket, but I've noticed that I can type for somewhere between 4 and 16 hours (depending on how well fed and watered I am before going "into the zone") without noticeable wrist problems. On a "normal" PC keyboard, I need to take a short break every 45 minutes or so, otherwise my forearms start feeling as if they're about to cramp up.
Anyway, when it comes to ergonomics, if it feels good, it probably isn't bad. Experiment with various keyboards (layout, mechanical construction, positions, sizes...) and other things that are somewhat easily changed. Try to stay with a change for at least a week, since all change tends to feel "bad" and "odd" in the beginning. Above all, consult an expert in the area and don't rely on hearsay from the Internet (but do take inspiration from it and find new possibilities to ask said expert about).