WebMD compiled an excellent list of exercises to do while sitting at your desk. It can be found at the following:
Stretching Exercises at Your Desk: 12 Simple Tips
If you’re like me, most of your waking hours are spent at a desk. One of my biggest weaknesses is flexibility. My hips are rigid, my shoulders suck, and I have neck pain regularly. I see a chiropractor and get a massage every week, but that’s still not enough.
To continue improving, I try to stretch as much as possible. Not only does it help my body, but it tends to help me think as well. Sometimes when faced with a difficult problem, I take a stretch break to help loosen things up. More often than not, I come back to approach the problem with a much clearer head.
Stretch for a bit. It helps more than you could imagine.