The Neo Geo roms will be identical to the MAME ones because MAME added emulation of Neo Geo arcade machines by merging the Neo Geo emulators Nebula and KAWAKS into it a while back. Although I still recommend you give Nebula a try if you haven't yet as it does emulate some of the Neo Geo games slightly smoother than MAME does.

As for the nonMAME set, this is strightly only games that made it into the arcades, and is a collection of all known Arcade game emulators that emulate games not currently supported by MAME itself, or for while other emulators currently emulate specific games better than MAME currently does.

Have you also heard of MESS? This is like the home system equivalent of MAME and the projects aim to to eventually enable MESS to emulate all know home systems in a single emulator. And in addition there is a nonMESS set that is a collection of everything currently not working or emulated in MESS.