PyMol is my favorite program for protein structure visualization. It is Free Software, and I just saw a video about how some people from the University of Toronto have used PyMol to make a module to implement "Head tracking" for giving a 3D feel to looking at the proteins.
The video doesn't give such a great impression of how it will be. But it is really nifty if the head-tracking-by-webcam works.
Here is another video that gives a great impression of how head-tracking (by Wii-mote) works.