(1) Switch to the Colemak keyboard layout -- it significantly reduces the work your fingers have to do.
(2) Vary your mousing devices/behaviors. I love Kensington trackballs, and they're much easier on my wrist than a mouse, but after awhile I get pain in my thumb (because with a trackball you typically use your thumb to left-click rather than your index finger), so I switch back to a mouse for a few weeks. Vertical mice are also nice and I occasionally use one for a change. You can also move your mouse/trackball to the other side of the keyboard and use your non-dominant hand -- it takes a few days to rewire your brain, but it's another good way to change up your mousing behavior.
(3) Consider buying a USB numeric keypad, placing it on the non-dominant side of your keyboard, and using macro software to program the keys for common actions (e.g., scrolling).