I got tired of the jumbled mess of jumper wires, so I started thinking about a pincushion, but that would just create even more clutter on my desk. I happened to have a hook in the ceiling over my desk, so I used a couple of "practice" ping pong balls and some fishing line to create these great holders for my jumper wires. The fishing line is poked through the ping pong balls and tied at each end, and the line is just hanging from the hook so the balls counter-balance eachother. There's enough friction on the hook so that the balance doesn't have to be perfect.
One tip -- push in the jumper wires from the top to keep them from dropping out, but otherwise, there's enough friction to keep the jumper wires in the little holes you form poking them into the balls.