Get a decent adjustable chair and some funny eco-hippe-new-age-sitting implement. Switch between them. I have an "office" and a "normal" chair, they are different enough so it helps.
Reason: There is no single position of your body that is healthy for a long time, but changig between at least two positions already helps a lot.
Get up when you can. I don't say "every twenty minutes" because that may conflict with staying in the flow. Pee breaks are not frequent enough for most men. I impulsively walk to another room when thinking about a problem, so I get the "get up" done frequently.
Put something you like on a far wall that you can focus your eyes on from time to time. A window into a garden behind the monitor(s) would be perfect for that, but that gives bad lighting condition, and garden isn't always available ;)
Monitor center should be slightly lower than your eyes so you slightly look down - this closes the lids a bit and eyes don't dry out that fast.
Don't skimp on the keyboard. the $9.95 model is not meant for people who spend hours typing. It works, but it is highly unlikely that it's good for you.
I never really liked ergonomic, but ended up with a decent cherry keyboard and preferring one of those tiny laptop mouses. They break fast in my hands, but feel good :)