I can’t remember now where I found out about this great tool but I use the 3GP_Converter to convert just about any file format that I can play on my PC on my iPOD. All I need to do is drag and drop the videos onto the converter and, when it’s done, they are waiting for me on my iPOD.
It’s a good idea to pick a storage folder for the output videos in advance (I just called my “My iPOD videos” in my “My Documents” folder).
Remember to delete the videos from the folder after you’ve removed them from your iPOD. If you delete something from iTunes and you *don’t* get that warning dialog asking if you want to send the file to the recycle bin then you’ve either disabled that dialog (re-enable it now!) or the file is still on your system.