With the MQ3 I sometimes use a Bluetooth mouse and keyboard and put down the controllers. Works fine.
That said, every "floating windows" application for the MQ3 I've seen has a terrible awkward interface for placing windows, everybody from Karl Guttag on down have noticed this and suggested many mechanisms that might be better (say point a beam somewhere to put the center of the screen somewhere, use the thumbstick to rotate and scale) but we are still stuck with bad UIs. This is one area where AVP has really done better.