Well, there would be only one rom per game (with original name), so I'd have to choose the closest to the originals.
At the moment there are 211 NTSC roms from which 75 are prototypes. the rest 136 are originals.
I could start at some point as you said in different folders, but i dont think it would make much of a difference.
My compilation is just PAL friendly.
Again, this is just a thought.