mvPod is a user friendly application to convert mostly any video into specific video format compatible with mobile device like iPod. Preset setting can be use to convert easily your videos.
I used to convert videos with Format Factory but I found this one better. Both free, but videos converted with FF double its length in iTunes. Everything is great with this app.
Very easy to use - just remember to install all the dependencies (mencoder, mplayer and gpac) and you're away.