ffmpeg2theora is a command line based Ogg Theora video encoder. It supports a variety of file inputs (courtesy of ffmpeg), and produces OGV files with Theora and Vorbis video/audio streams.
For those that need a GUI, FFCoder supports ffmpeg2theora.
Updates for version 0.25:
fix input from codecs where width/height is not encoded width/height
fix a/v sync issues with some mov/mp4 files with strange framerates
add new option --info outputs json info about source
frontend mode outputs one json dict per line now
select video stream if input has more than one video(--videostream N)