While the iPod can read the .mov file format, the video contained inside has to be in either the MPEG-4 or H.264 format, and within certain specifications. MPEG-2, even in a .mov file, needs to be converted to MPEG-4 or H.264 before it can be moved to the iPod and played successfully.
QuickTime can play MPEG-2 content, but only with Apple's MPEG-2 QuickTime component, available at
http://www.apple.com/quicktime/mpeg2/ . The MPEG-2 component can also allow QuickTime-based applications to export to other formats, but will only process the video portion of the original file. The audio in plain MPEG-2 files is muxed, which means it is mixed into the same data stream as the video. QuickTime treats that data stream as a single QuickTime track data structure, and does not have a mechanism for extracting the audio separately. This presents the same symptom in almost every QuickTime-based video processing application: exporting from MPEG-2 will produce files that look fine but are completely silent.
Podner works around the MPEG audio limitation in QuickTime by employing ffmpeg, an open source audio/video processing engine, for audio extraction. Podner then uses a couple of resynchronization techniques to apply the extracted audio, after it's converted to AAC, to the final video output. The result is typically usable, but can exhibit audio synchronization issues if the source material is not pristine.
Other consumer-level applications that can work with muxed audio also display similar audio/video synchronization issues. Our tests show that Podner's synchronization success rate is somewhat better than that of utilities that are entirely ffmpeg-based. These tools usually allow ffmpeg to process the audio and video simultaneously or, using other methods, simply place the audio and video together at the last moment without attempting to resynchronize. There is one tool that can produce better synchronization than Podner: MPEG Streamclip, available at
http://www.alfanet.it/squared5/ . Its output can still be poorly synchronized, but tends to sync better than Podner under some circumstances. MPEG Streamclip also requires the QuickTime MPEG-2 component to process MPEG-2 source material.
Because some iPod video tools are not based on QuickTime you might find that they work with MPEG-2 content. Search for "iPod video" at VersionTracker.com to see a full list of iPod video tools for the Mac.