With Blizzard’s help, I figured out an ffmpeg command-line to convert to H.264 encoded video and AAC encoded audio in an MPEG-4 (mp4) container. This is supported by Aperture 3 and other Quicktime apps.
$ ffmpeg -sameq -ab 256k -i input-file.m2ts -s hd1080 output-file.mp4 -acodec aac
Command-line order is important, which is infuriating. If you move the -s or -ab arguments, they may not work. Add -deinterlace if the source videos are interlaced, which mine were originally until I turned it off. The only downside to this is that it generates huge output files, on the order of 4-5x greater than the input file.
Update, 28 April 2010: Alexander Wauck emailed me to say that re-encoding the video isn’t necessary, and that the existing H.264 video could be moved from the m2ts container to the mp4 container with a command-line like this:
$ ffmpeg -i input-file.m2ts -ab 256k -vcodec copy -acodec aac output-file.mp4
And he’s right… as long as you don’t need to deinterlace the video. With the whatever-random-ffmpeg-trunk checkout I have, adding -deinterlace to the command-line segfaults. I actually had tried -vcodec copy early in my experiments but abandoned it after I found that it didn’t deinterlace. I had forgotten to try it again after I moved past my older interlaced videos. Thanks Alex!