I
think that when you rotate a .mov in Quicktime and then SAVE it, no re-encoding is done. Instead, the display settings are set, so that the movie gets rotated "on the fly" when it is played back. The good news is that you don't get lossy reencoding. The bad news is that you have to spend the machine cycles to rotate the image during playback.
If you EXPORT the rotated movie, then you will re-encode. So if you are producing sideways movies, do as little transcoding as you can until you're ready for your final export, then do the rotation and export the rotated movie using your distribution compression method. For example, I'm working on a project that I shot in DV-25 that needs to be rotated. I'm going to either turn my monitor over, or work lying down until I get the editing done, leaving me with a DV-25 encoded project. I'll rotate that in QuickTime and then export the rotated video to MPEG-4 or H.264 for distribution.
That was exactly the workflow I used for this test clip, encoded using the 3ivx MPEG-4 encoder:
http://capital2.capital.edu/admin-staff/dalthoff/rrc/dragmagnum.mov
You can "open URL" in QuickTime for more details. The encoding loss you see is first-generation MPEG-4 loss caused not by the rotation, but by the encoding to MPEG-4; that is, it would look pretty much exactly the same (although because of the way the encoder works, the encoder errors would be different) if I had not rotated it.
--Dave Althoff, Jr.