I usually sit with my feet on the desk and keyboard in my lap (by far the most comfortable position I have found for long days of typing), but it does cause circulation problems in the legs, which is why frequent breaks are necessary. Fortunately, I’m busily working on a solid nicotine addiction to keep me taking those breaks.
Unfortunately, I work for an extremely large corporation, and we have crappy chairs and little to work with in adjusting monitor height. In fact, the monitor itself would be intolerable had I not put it into a requirements list for a piece of software I wrote 8 years ago.
Our keyboards, mice, and monitors are typically the low end of whatever Dell offers with their computers, so I have my own MS Natural keyboard (an older one that I used to use at home before buying the MS wireless Natural), and an MS Trackball Explorer (http://www.amazon.com/Microsoft-D68-00007-Trackball-Explorer/dp/B00005853Z), which MS no longer makes (in fact, they don’t make any trackballs last I checked). Using a mouse severely inflames the carpal tunnel in my right arm, and using a straight keyboard makes it impossible for me to type for more than 2 hours a day (due mostly to having broad shoulders, as far as I can tell, but then I don’t really know how anyone can type on a straight keyboard for hours on end).
My only other problem is that I have a tall torso, which makes ergonomic seating harder to find (and makes non-adjustable seating very painful over long periods, such as airplane seats).