HandBrake, an Open Source video encoder
HandBrake is a simple, open source program designed to convert videos, movies, and obscure media files into formats that can be read by various devices such as the iPod, Apple TV and others. In this tutorial, we'll show you how. You'll be converting videos in no time!
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An article detailing how to transcode files would be helpful too. Some devices have issues depending on the options you select when ripping a video.
Also, maybe a link to some good presets would be nice.