For myself, using the NES and SNES emu's I whittled the 8000+ and 6000+(respectively) roms down to about 600 for each of them, that is whats kept in the playable directory. Ive got the full sets zipped up on a disc, and its just 1 rom per game, no hacks or alternates or country specifc where possible.
Once I had my 'good' set I renamed everything without the () and [] stuff at the end, did the same with the snaps, and it's fine
THis is using advanceMenu. I think there might be an option to trunc the display name after ( but im not sure