Good question!! I have been obsessing over this for a few weeks now. I may be completely wrong here, but I have been told that all you have to do is change the file extension from mov to mp4. (And the same with a FLV file?)
MP4 (with extension .m4a) is a Lossless codec. They have a pre-set for this in Compressor.
H.264/MPEG-4 Part 10 is a Lossy codec and this is what I think my clients are asking for when they say mp4. They have many presets for this in Compressor.
Vimeo also wants a H.264 codecs with the file format as mp4. Is this also just a matter of changing the extension?