There are many Unix tools to re-encode and convert video and audio. But you have to really know what you are doing to use them. Fortunately, FFMpegX provides a great Mac interface to those tools. We use it here at MacMost to encode all of our video episodes into mp4 format. You can use it to convert video to work on your iPod or iPhone. It also compresses a lot better than QuickTime Pro or direct export from most video tools.