Large screens and frequent short breaks are the key to me. For CRT's the glasses I wear I pay extra for a coating that blocks some light specially made for heavy computer users (I'm a software engineer - no real choice). I go to the water machine, candy machine, coke machine, something several times a day. Usually whenever I hit a good break spot in whatever part of the software lifecycle I'm doing - and I take a short 5 minute break at *every* one of them. It also helps maintain concentration all day to have those short breaks.
Though recently I switched to LCD monitors and like it a lot. Personally I feel better with a dual monitor setup when I can afford one (or the employer will provide one). Not really that useful for gaming, but code in one monitor and output or reference guides on the other means I refocusing and generally moving enough to feel better. Most computer heavy jobs can benefit from dual monitors both in terms of production and ergonomics.
For me, the largest problems is finger joints. I used to be really rough on keyboards due to hitting the keys hard (still am hard on them to some extent but for other reasons, though most gamers know about wearing WASD, ctrl, alt, and a few other keys out quickly

). I've never really had great joints (they pop and crack too much, a little arthritus in one joint by about 27-28 years of age), but I did some real long term damage to them.
Though, for long gaming sessions you are probably doing more damage from not moving your legs than anything (assuming that your keyboard, mouse, and monitor are properly placed, which just pretty much means comfortable and most of us do that anyway). I know I'm not the only one that gets into a game and finds I've sit totally imobile except for my hands for well over 8 hours from time to time. That's actually dangerous and can kill. While rare, as my generation ages (30-40 age - the "Nintendo generation" or "Atari generation" - whicever you prefer) it will become a bigger issue. I know that after a particularly long gaming session my left knee and right ankle is sore for about ten minutes after I start moving. It's not anything close to bad but will only get worse as I age.
Amusingly enough I like the "You have been playing for 1 hour" message many have complained about, I wish there were more games that did it. I remember to move a bit during long gaming sessions when it pops up, though I don't think that's why they added it.