I don't have an ipod myself but from what I hear the only format supported is mp4. One alternative is the AVS Video Converter which seems to support most formats, http://www.avs4you.com/AVS-Video-Converter.aspx. I haven't tried that specific one myself. I personally use the AVS Audio converter to change my mp3s to FLAC and it's very userfriendly.
Well I heard that itunes has this function as well (only heard, never practically operated!!!). It saided that when you put the video in iTunes and right click the video you put in the “video section", there should be an option “convert for ipod” or “convert to mp4” that can help you make it. You can try on this.
And if it didn’t work, I suggest you use Video Converter Ultimate, it’s easy and fast, for mac you can use Mac Total Media Converter
This is a thread-necro from May this year. I'm fairly certain the OP has found a nice software to use since. If you are looking for something specific, I'd recommend Any Video Converter which is free and comes with iPhone, iPad and other, useful presets.