MOV is the best one I know of and is generic (MP4 might not be, the spec 14496-14 isn't public so I'm not sure). The only thing I don't like about it is that the index comes at the end and is required to play the file, so you either have to write the whole thing out twice or you can't play partial files.
Something like this will probably be added to the article soon, I think he's researching it better than I just did.
This is really a problem with the GUI defaults. Assuming you're using MPlayer OS X Extended, set Preferences -> Video -> Framedrop "Soft" and "Use multithreaded ffmpeg build", and it will play faster than any other OS X player. (excluding CorePlayer of course)