I can confirm that even with the Nvidia 3D Vision system it does put strain on your eyes. But, and it's a big one, it does not HARM your vision. I've done some reading up on this and so far all of the studies done have shown that it just stresses your eyes - but not in a harmful way. Some older folks who are use to eye strain due to age don't even notice the effects of 3D media, so it's like comparing an athlete to a couch potato - the couch potato will sweat running up a flight of stairs whilst the athlete won't even notice.
I have found that I can only play for a maximum of about 1 hour before I need to take the glasses off. I've also come to the conclusion that wearing glasses to play a game where you need to have super concentration (like Starcraft 2) does get annoying and I find myself always playing WITHOUT 3D Vision.