A buddy of mine and I were recently playing around with making color photo anaglyphs. Anaglyphs are the names of the pictures that you view with the red and blue "3d" glasses. He found a program on the net that would help make the pictures and compile them into a single picture. It involved creating layer masks of your photos and then processing them through this application, which would then create the proper red and blue lines in the picture to apply the varying degrees of depth. It actually worked ... .pretty well.
Stereoscopic 3d imaging, what you are doing with the two pictures side-by-side is pretty cool too and I've been meaning to try some of that out as well.
Thanks for reminding me!