Need more data. A few questions and I am sure there will be more.
My iPad plays 3D movies. I recently watched "House of Wax" and part of "Robot Monster." Not stereoscopic versions, but a 2D releases. I also have watched some 2D versions of classic 3D films released by Castle on 16mm film transferred to digital.
So are you asking about watching non-stereo versions of 3D or do you want to see the films in 3D? I am guessing you want to view the movies stereoscopically. The problems you face are great. If the film is displayed in a format the device can handle, and you are equipped properly, yes, you can.
There are many different stereo formats and techniques. Anaglyphic, polarized, Pulfrich, ChromaDepth, various glass-less systems, LCD Shutter, lenticular, etc. There are interlaced films as well. All of these formats require either special adapters or special viewers. For example, anaglyphic requires red/green or cyan/red glasses but they are easy to view on the iPad. Polarized systems are a no go, and unless you can find the required software for handling interlaced video, that is largely a no go.
If the 3D film was a created to be viewed with a polarized system, then you can watch the side by side stereo pair using what is known as 'free viewing.' Search the web for info about this. Easy to find because there are thousands of stereo enthusiasts out there, and they/we have been making stereo photos for a very long time, so there is a great deal of information. I actually shot 3D professionally as well as processing, printing, and mounting 3D images during my time with Bill Shipler Photo here in SLC. I know a few things about this topic.
If the film is anaglyphic, then it is easy to view on the iPad. You just require the requisite glasses and your good to go.