Seriously, screw Theora. None of the tools work. Really, there's no reason to go beyond that at all. ffmpeg can't create working Ogg Theora files for no discernible reason. The makers of Theora don't provide an encoder, so it's not like you can just use theirs! The only working Theora tool appears to be ffmpeg2theora - which is completely useless because it can't be used to remux streams.
The one thing Xiph does provide, a tool for creating Ogg streams, doesn't create working streams. Making it completely useless as well.