3D input devices, like those from 3dconexxion, run in 2D. They sit on a flat surface as you push, twist, and tug them to simulate 6 axes of motion.
Engaget is reporting on a true 3D input device unveiled by Noint at the consumer electronics show running this week in las vegas.
Novint Falcon crazay mouse gets a price, release date notes that the price is US$239, it ships in June, and that it operates like this:
...the basic gist is that the Falcon features a floating doohicky attached to a pod doohicky, and the floating part moves about in 3D space for controlling video games, 3D modeling programs and the like. The real kicker is the force feedback that's been worked into this thing...
The problem with this device may be that you have to keep your hand, unsupported, suspended in the air -- one of the reasons touch screens never became popular.