Have you seen a 3D movie file? You don't even stitch the files together, just put them side by side in the right resolution, most 3D cameras and processing software would probably do this for you anyway.
(For those who are still confused)
Here's an example:
http://www.youtube.com/watch?v=wDZfa9oBsoA pause at about 10 seconds in, then click left image on the 3D menu, then click right image only... flicking through the two shows a slight difference in perspective. Without the 3D movie tags this is a single movie file with the aspect ratio of 42:9 (two videos running side by side).
original movie file:
http://http.download.nvidia.com/vide...Quest_576p.wmv
circular polarisation, every 3D is tricking the brain, but it's more about how your eyes receive the image. The glasses are only to put the images back together after they've been separated, putting them back together at the screen means no 3D, but putting it together where your eyes are makes use of the space between you and the screen.
http://en.wikipedia.org/wiki/RealD_Cinema