Have you ever done focus/tension exercises? Basically, you start at your feet....tighten all of the muscles in your feet as tight as you can, then relax. Move up to your calves, upper leg, rear, core, shoulders/arms, neck, mouth, forehead...tighten each one as hard as you can, then relax it. Breathe throughout.
It makes you aware of body tension, relaxes your muscles, and can be done entirely while seated at your desk.
i sometimes do meditative breathing - somewhat along the lines of what Mandalinn suggested, but i can't maintain that focus <gotta work on it>. but even a few minutes of BREATHING helps - more than i ever thought possible.
Have you tried isometirics? http://entrepreneurs.about.com/od/li...skexercise.htm
these are specificly for offices, when you find yourself really craving something try a set of these, that way you are involved physically, dont have to leave your cube and are keeping yourself healthy.