I saw a DVD in Rebel Sport the other day that had a whole section on workouts to do at your desk... should have bought it
I'm stuck at a desk too, and really don't know about any excercises. I drink a heap of water so I get excercise going to and from the toilet!! And I go for a long walk at lunchtime, about 30 - 40 mins.
I have a friend who sits at her desk on an exercise ball. I think this is a great idea because you will be burning up way more calories sitting on the ball rather than sitting on a chair. Just gotta put up with the flack from your workmates... but they'll get over it