Shadow Locked makes a great point about how a 3D movie, Avatar especially, doesn't gel with our perception of the world. Check out their tips for how to get through Avatar without getting a splitting headache.
The author argues that when we're presented with a limited depth of field in a movie, we're trained to focus on the blurred section of the frame. That's where directors traditionally hide details.
When we're looking at a shot that has a limited depth of field in 3D, though, we expect to be able to shift our gaze and focus on that blurred area. But instead of seeing that part of the frame clearly, it remains out of focus.
I can see how that could be disorienting for some people. I've never had a problem with it, but I know people who have. Hit the link for a full rundown of how the author managed to control his headache. [Shadow Locked - Thanks Martin]