HandBrake is easily one of the better video transcoder open source free software available. It is especially Apple friendly as it comes with video out presets for iPhone 4, iPad, Apple TV 2 etc, making video codec/framerate/ crop ratio settings selection a non-issue for those less technically inclined.
HandBrake 0.9.5 has just been released, and this is more than a year since its last 0.9.4 release in 2009 Nov. The new release has lots of new features and bug fixes. PowerPC Mac is no longer supported in this new release.