I went way beyond the wrist pain and deep into the territory of surgery, disability, half a year of near-total inability to use a computer, and am finally back to what most people would call a 'normal' life.
I work for a games company and am at my desk about 50 hours per week. On top of that, I spend another 20-25 per week on a computer at home. Add in some Playstation time, some XBox time, and a smattering of a musical instrument... and it's amazing that I am back to nearly 100%. How do you go from useless to lead programmer in a year or so?
You asked about equipment, so I'll get to that, but dropping bucks on hardware won't make it all go away. When my surgeon told me to get away from the computer 4-8 times per day for 3-5 minutes of circulation-restoring activity. Well, I took up juggling, but 1) you may not take to my brand of physical therapy and 2) your company may not either.
Get some exercise. Seriously.
NOW I'll deal with equipment. What they say about the ergo layout of your desk is subject to the 80/20 rule, just like everything else. You get 80 percent of the benefit from 20 percent of the layout. The placement of your hands is the big one. I still slouch, I sit on my feet, and my keyboard is up on the desk, but I'm still getting most of the benefit for the least discomfort.
The really important bits - get a keyboard that straightens your wrists AND doesn't force you to tension your tendons to elevate your fingers. That right there means a contoured keyboard. I love both the kinesis and the maltron, but the kinesis' function keys drive me crazy. Since I have the keyboard on the desk, I prop its rear up about an inch so my wrists are straight. I also use an evoluent mouse, and that really helps when I am spending an hour or two... or ten... mousing.
Your hands are your future in this business, so don't *#(@ around. Get your layout set up so that you're comfortable and take some time off - away from the computer, the texting, the game controller, the DS, and everything else that makes your fingertips tingle, and get on the ibuprofen for a while. During this time, see a professional and insist upon getting an EMG. My hands hurt like hell, but I never thought it was that bad until I found that my nerves weren't working the way they should.
Oh, and make sure that you opted in for the full disability benefits plan at your company. Best decision I ever made. Well, I also switched to Dvorak, but you may not be that crazy.