Hi I just found this page through Google and wanted to add my Two Cents.
I have Nystagmus and I have tried many times to watch 3D movies. In the majority of cases it outright does not work.
When using the polarised glasses from the cinema I find it does not work, reason being for me is because one eye is weaker than the other, I do not know if this is the case for all people with nystagmus but for me it is and I assume because of that and because my brain relies upon one eye more than the other the stereoscopic light trickery of polarised glasses outright does not work for me. As for the Red / Blue 3D Glasses with 3D Images and on PC Monitors I have more success with them but again it is incredibly strained and no pleasant at all.
For me I simply avoid 3D altogether. I am curious about the new Nintendo 3DS though and whether it would be any different as it does not require 3D Glasses but I am yet to try that out.
A world exists beyond the Horizon just because you can't see it doesn't mean it's not there, seeing isn't believing, believing is seeing