Matroska is free and "okay". It has some technical annoyances (the authors liked a few codecs so much they made their own special complicated setups for them, the EBML parser is a lot of code) but does have generic codec wrappers and better seeking. It also has commercial support and several extremely practical tools.
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.