I ended up using ffmpeg and ffmpeg2theora.
WebKit compatible h.264 video
I decided to go for the ipod640 preset because it means the video can be viewed nicely on an iPhone or iPod touch. Of course, you can change the settings around a bit, get rid of the '-vpre ipod640', change the resolution or quality. Anyway the command is:
ffmpeg -i video_source_file.ext -vcodec libx264 -vpre ipod640 -b 250k -bt 50k -acodec libfaac -ab 56k -ac 2 -s 480x320 video_out_file.mp4
move some information to the front of the file so the video can play before it loads
qt-faststart video_out_file.mp4 video_out_file_quickstart.mp4
Firefox compatible Ogg video
This depends on you having ffmpeg2theora installed. Also, I have only tested it with the input file being the output file from the previous ffmpeg conversion. The command is:
ffmpeg2theora -o video_out_file.ogv video_out_file.mp4
