how about MAME, which has a zip-based format containing raw ROM dumps, and the "CHD" format for disk/disc based media? obviously all of the metadata is still contained within MAME itself.
Also, even MAME is not immune to political ROM-format problems. The format MAME used was designed to help people maintain and update arcade boards, which often had the ROM chips socketed so they could be replaced by the end user and so "a set of ROMs for a game" was a reasonable thing to talk about. MAME uses that format for every platform they support, but most home consoles were not designed to be end-user modifiable, and sometimes the same game shipped on different sets of different sizes of ROM chips (say, a 4Mbit chip, or two 2Mbit chips) depending on what was cheapest at the time.
MAME as a collective project doesn't have the will to use different formats for different platforms, and home-console emulators aren't interested in following MAME's arcade-based conventions.
I'm not saying the MAME approach is wrong: every approach has its pros and cons, regrettably.