In addition to keyboard and mice, of course extra monitors are likely the most important component here, in terms of number, size, and alignment.
Here are a few tips (from my own experience):
IMHO, the most important thing is aspect ratio. If you use an IDE (Eclipse/Visual Studio/etc.), I would strongly suggest that that your main monitor, the one showing your IDE, will be a widescreen. Most IDEs have a side-by-side structure, so it's super useful to have things like an outline or package view on the left and still enough space to see all the text. I am personally a fan of a 16:10 (like 1920:1200) over the HDTV 9:10 ratio.
Second, of course, is real estate. My vision is crap, but development is one of those things where you can't go wrong with extra space. My workplace supplies 20". I bought my own 26.5" 1920x1200 monitor for less than $300 and it really makes life difference. If you aggregate it over the time you spend in front of the monitor, it's worth every penny. Since you're coding, you could do well with any crappy TN panel. You don't really need perfect color reproduction for Eclipse or Visual Studio. So ignore the typical reviews or look for reviews on NewEgg where people discuss what they used for Dev.
Third, once you get a monitor, adjust the contrast (and the backlight, if you have access). Most monitors are configured out of the box to look good, and produce enough illumination to secure a parking lot in a shady neighborhood. Tune down the contrast to what is comfortable for you, and adjust throughout the day.
Fourth is color - A monitor is essentially a lamp that you stare into. Most IDEs use a white background. I found that I get a lot less eye fatigue by using a black background. On a mac, you can simply reverse everything in the "universal accessibility" config. On windows, your GFX card provides a setting to invert the colors. I keep my IDe monitor in an inverse. Be aware, this looks like crap, and you have to get used to a whole bunch of colors (e.g., red is now blue). Once you do, however, you might find your tolerance for staring at a monitor increasing tenfold. You may need to increase contrast, though. I keep my secondary monitor with normal colors.
If you follow the reverse contrast thing, check your glasses - if you use multifocals (some folks like myself do) and ,they get to be messed up around the edges.