Here are working QuickTime Pro MPEG-4 Export settings for iPod video.
UPDATE:
I just figured out a better way to do this.
From QuickTime Pro, you choose to export as a MOV, but then click on the options to use the MPEG-4 Compression type. This puts the mp4 file in a mov wrapper. That keeps you from having problems playing the mp4 file type. More details on this later...