Having played around with various stereo methods in the past (including both anaglyph and LCD shutter glasses) I would suggest that polarized light is definitely the way to go. 'All you need' is an extra monitor and a sheet of half-silvered glass and you can build yourself something like this:
http://www.aldous.net/photo/project08.htm
And here's a slightly more elegant commercial version:
http://www.planar.com/products/flatpanel_monitors/stereoscopic/index.html
EDIT: I just remembered where I originally found the links above. Here:
http://forums.nvidia.com/index.php?s=d2f721a5312adf0fba8fc49b73c919a1&showtopic=32547&st=0
http://www.aldous.net/photo/project08.htm
And here's a slightly more elegant commercial version:
http://www.planar.com/products/flatpanel_monitors/stereoscopic/index.html
EDIT: I just remembered where I originally found the links above. Here:
http://forums.nvidia.com/index.php?s=d2f721a5312adf0fba8fc49b73c919a1&showtopic=32547&st=0