I've tried Lives, KDenlive, Avidmux, Openshot, Pitivi, and Cinelerra, and I cannot figure out how to merge two movies into a single movie. Cinelerra no doubt has this ability due to its complexity, it just really needs a UI overhaul and lessons in usability since it takes forever just to figure out how to do basic things with it.

Someone made a script to use gStreamer to combine videos here but even after installing the ugly plugins from the multiverse repo on Ubuntu 10.10 so that I have x264enc, I still get the
Code:
Pipeline is PREROLLING ...
of doom, which just sits there waiting and isn't actually doing anything, a common problem with gStreamer apparently...

If mencoder can do the same thing I haven't figured out how.

Does anyone know how to edit movie frames so that you can stick the second video into the same frame on any video editor for Linux out there, or know of a way to use a command line encoder to do so?

I have two 1080p movies that I'd love to be able to merge, creating either one 3840x1080 movie or a 1920x2160 movie.

You'd think there would be more Linux users out there using dual cameras to create 3D movies. Having such a tool is necessary to get this done so that they can be displayed on a 3D TV, or by one of the new fledgling Linux 3D movie players (when is VLC, Totem, or MPlayer going to pick up this support??).