I used a crappy NES emu for a while now, and because of the slow rom load I organized all my roms into "A-D" "E-H" etc. folders in GPMM/NES.
Now I have the new little john and I would much rather have all the roms in GPMM/NES without all the subfolders.
I use Comi.fxe to move files in my gp32...