<shameless plug> I am currently/slowly developing some software that will do just that - TigerPod. It's written in .Net, uses ffmpeg and will be complete freeware. I have tried all the shareware convertors out there and they're all complete crap (imo), hence creating my own...
If you are referring to my TigerPod, it's not available for download right now -- I still haven't put together an installer package (which, in all honesty, will consist of a ZIP file with the tigerpod.exe and a copy of ffmpeg.exe).
If you really want to try it (it only accepts .avi files right now), then there are instructions on the website on how to get it.