The modern solution is "shutter glasses"

An example here

You have a high refresh-rate monitor that displays both images alternately. Then, the shutter glasses are synced to the monitor (here by a cable, but with more expensive products, by wireless IR). The shutter glasses alternately polarize out one eye, so each eye sees only it's half of the image pair.

In this way you can get full-coulour 3D without any eyestrain.

I've used them in a number of professional 3D simulation packages and they are really great.

(And if you want to the whole visionarium thing, you gott try a force-feedback manipulator- it feels just like you're pushing real objects around)