I use 3D vision, and do not get headaches as long as you can maintain 50+ FPS (which I always make sure I do).
That said, AMD doesn't use 3D vision, it uses HD3D and neither systems will work well with a TV due to connection limitations.
One of the major reasons I choose 3D vision (or HD3D) is that I get motion sickness and headaches with low FPS and having over 60 FPS improves the issues a lot. At 90 FPS I get no motion sickness at all. Going Eyefinity makes maintaining even 60 FPS much harder. With a 120hz monitor, I either get 3D or high FPS, both of which are desirable for me.