3D in the theatre never ever has given me a headache, though I did feel like I was going to suffer an embolism in my leg about 3/4 through Avatar. I had to stand in the aisle for the about 20 minutes before I could sit comfortably again.
However, every single time I have demoed a 3D television in the store, within a half hour I have a pounding headache that lasts the rest of the day. Either the screen wasn't big enough, or too much background reflection, or something out of adjustment, or just my brain can tell the difference between polarized light and flickering shutters, who knows.