You might try to take pills for headache half an hour before the movies.

You'll still get headaches, but won't feel it. The trick works for me.

It's a bit crazy to have to medicate to watch a movie comfortably, but that's the only way I manage to work on 3D stuff for more than 30 min or so without getting a splitting headache, even with the top notch pro glasses that are supposed to spare you those (thankfully a lot of the graphic work I have to do on these movies can be done by entering numbers instead of working visually, at least when the studios bother to provide us their z-depth info. I hate that stuff, that's totally counterintuitive. You need to offset the position of an element to the left or right on one side, or on both, to adjust its position back and forth in depth. I get headaches from that too!).