You should stand up once in a while when working on your desk to avoid sitting for prolonged periods of time and causing problems with your health. But if you must sit down, you can still get your blood moving using an elliptical trainer under your desk like Stamina's InMotion E1000 Elliptical Trainer. However, the E1000 is designed for standing up so you might want to tilt it towards you to properly use it when sitting down. Or the Cubii, which claims to be the world's first “Under-Desk Elliptical Trainer.” This sleek-looking device allows you to work your lower body while you work without distracting you from it It syncs with a mobile app via bluetooth so you can check out your stats and get excited about doing better. The app also takes data from other fitness trackers so you don't have to use multiple apps. The best thing about this is it keeps you awake at work.
This product was successfully funded on Kickstarter but it seems some still have not received their Cubii. We advise against trusting Kickstarter projects from our own experience.