After a decade of Emacs, I never had wrist problems, but I did end up developing pinky problems, due to remapping Ctrl to Caps Lock.
I tried foot pedals (and still have them under my desk). They were better than nothing, but after I switched to the Kinesis Advantage keyboard I ended up not using them anymore. Hitting Ctrl+Alt with your thumbs is more convenient than hitting them with your feet, especially since I tend to fidget a lot. Another advantage (no pun intended) is that the arrow keys are convenient to hit, which lets you remap several standard Emacs keybindings. For example, I use C-b to switch buffers.
Neither switching keyboards nor using foot pedals solved my hand pain, however. I ended up having to take more drastic measures: I switched to the carpalx QGMLWB keyboard layout[1]. One of the advantages of the carpalx approach is the clear and powerful mathematical model which quantifies the effectiveness of keyboard layouts. I was able to select a layout that minimizes pinky strain--if I had switched to Dvorak or Colemak, I would have increased my pinky strain.
> [B]ut the keybindings are horrendous. Even if they don't cause hand pain they're long-winded and distracting.
Ha, after 26 years using Emacs I find Vim's keybindings long-winded and distracting. To each their own. However, unlike many people I don't dismiss vi because of unfamiliarity, or use them as an excuse not to learn the editor. I try to use it all the time, but I can never seem to train myself to do non-trivial things with it.
I have the similar problem with other editors: I've seen people rave about Sublime Text, yet none of its killer features (modulo multiple selections) really strike me as worth switching. And any of its features I think I want I could (conceivably) implement in Emacs, so...
If you are emacs user, that's not a problem. You just change them to whatever you want. Besides, food pedals is not so crazy ideal. Any time you must do something meta- or control with any software, you end up doing movements that are not so natural.
I use my thumbs for control and alt on a regular (scissor type) keyboard. I remap alt to control and super to alt and have had no problem since I switched, about 4 or 5 years ago.
A: Foot pedals.
http://bc.tech.coop/blog/041024.html
http://www.cb1.com/~john/computing/emacs/handsfree/pedals.ht...