How would the glasses help in this case?
http://techcrunch.com/2011/07/22/who-could-have-guessed-3d-hurts-your-eyes/
For me it's not so much as a headache as my eyes hurting and I noticed it in the last 15 minutes or so when I watched wreck it ralph in 3d.
I wasn't saying any particular type of glasses help; I merely stated my experience, with what type of glasses I had used.
At home, you'll more likely find active-shutter glasses. I believe some theaters may utilize this, but most theaters use some form of polarized glasses. That is, they are similar in application to the red/blue filter glasses, except the glasses tend to be a little more sturdy, and the filter both more effective and a better material that doesn't introduce visual distortions.
I know there, at one point (and probably still today), there were two types of polarized glasses in use in theaters. One was circular polarization, one was a straight directional polarization I think. I don't believe one could cause problems for an individual but not the other, but it is possible. I do believe it could be possible that passive glasses, using polarized filters, might be problem free, or even cause problems, whereas active-shutter glasses at home might produce the opposite result for an individual. I can't say for sure.
As for physical discomfort, again, that's a per-individual issue. Some will experience discomfort, as has been noted frequently, but others experience no ill effects (such as myself).
Part of the issue is proper seating location. Some seats are a) going to have diminished 3D effect, and b) increase chances of the eyes struggling to comfortably take it all in.
But other than that, if one does experience discomfort, I imagine a good bit of advice is be mindful of what your eyes are focusing on in any given scene. I think a good film is going to keep the ideal focal point at a neutral distance, with the scene enveloping said focal point. Of course, we like to let our eyes wander, look at various details and pieces of action occurring elsewhere in a scene. But if it appears blurry, it's probably not in focus during filming, and that means something else is in focus (the subject). If you don't wander and remain with what's in focus, you may experience less discomfort.
It's hit and miss - some people just won't experience discomfort. Or they may possibly have just a small bout, relax the eyes a bit, and they're good to continue on for another hour.
I've experienced discomfort just looking at a computer screen during gaming for long hours - it's not restricted to only 3D stereo viewing that's displayed on a 2D plane. It can be any 2D plane with moving imagery. Hell, it can even be the fully 3D world out there - it's less likely you'll find yourself darting your eyes all over the place, constantly changing focal point to and fro, close and far, so often that it introduces discomfort, but it can happen.
Don't take such articles as "omg 3D is bad for us!" - everyone has different capabilities, and 3D stereo can just bring out the discomfort faster in some individuals.