Handrake is an open-source video encoding program. It can convert to H.264 or Theora from almost any other format. It is used by many in the fansubbing community to encode videos.
You can find the user manual here: HandBrakeGuide ? HandBrake
Handbrake can manage a final encode of an epsiode in about 2-6 hours depening on the source file, settings, and hardware of the computer using it.
It comes with many tools, including powerful video filters, an easy-to-use GUI, and the ability to use preset or customized encoding profiles for various tasks.
A link to the forums: HandBrake • Index page