If you download the CLI ogmtools you can demux the streams to their "native" file formats (of course video and audio codecs don't have "native" file formats, but it puts vorbis in ogg files and xvid in avi files). OGM can hold any codec though, so you might end up with RM video or something else. If you can open the movie in VLC that's a good sign, hit command-i to see what codecs are used. Actually, if you can play it in VLC, VLC has a transcoding wizard and it can just convert the file for you. It would be better to demux with ogmtools (because it's lossless) and then convert to mp4 with whatever you want, since VLC will probably not give you something that's ipod compatible. But VLC will be more GUI oriented for you.
What exactly gave you "no luck" about ffmpegX?