I, for one, really like the idea of a single .zip file per game. Then you can include the unmodified ROM, a separate file with configuration data, any necessary firmware, box art, and any other information an emulator might want. And it saves a little space to!
Also, if two different emulators want two different configuration formats, you could just include both! (As long as the file names aren't the same.)
Also, if two different emulators want two different configuration formats, you could just include both! (As long as the file names aren't the same.)