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I would guess it wont be the software as the culprit so much as the codec and encoding settings. Though some footage will never compress well, and a few codecs are better suited to use in different scenarios.
Most "do it for me" encoding solutions leave you with a lot file size you could have trimmed while still preserving quality. As with any one size fits all kind of deal there is always a draw back. In this case the drawback is you could generally get better results by handling the encoding settings yourself.
If you are starting with .MOV I would be curious to know if the files is already encoded or in raw. If you re-encoded a .MOV file that is in H624 or similar to .AVI you will see quality degrade regardless of the program you are using. Though Im sure know that much if you are this far along in the process.
Streaming Media Magazine does reviews on encoding software all the time you may want to look there for a simple solution that yields good results.
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