I have a couple of exercise bands at my desk which I use when my hands are free. They don't take up much space, and you can get some with pretty decent resistance. You could also get a couple of ~8-10 pound exercise balls; tossing those from hand to hand can be a pretty decent light workout. Standard free weights are an option too.
Honestly, you're just not going to get a lot of cardio in while at your desk. But you can do some light strength training and toning, which will help keep your metabolism up a bit if nothing else.