Following Jamie's earlier posts to this blog (here and here), I downloaded and installed ffmpeg2theora and handbrake. Not sure exactly where the installer put ffmpeg2theora as it didn't tell me, but I was able to invoke it. I installed handbrake into the applications directory.

To create the ogv file, I executed from the command line:
find path/to/mov/folder -name *.mov -exec ffmpeg2theora --videoquality 6 {} \;

To create the mp4 file, I used handbrake's GUI, set the codec to H.264, the Video Quality to Constant Quality 20, and the framerate to Same as Source. I was unable to execute the same thing from the command line.