Here's how I accomplished getting 160+ roms on my CycloDS. Folders.
+
|\
| +Roms
|ÂÂ|\A
|ÂÂ|\B
|ÂÂ|\C
|ÂÂ|\D
|ÂÂ|\and so on
I put Games starting with A in the A folder, B in B, and so on. If a folder has more than 60 games, for example, the D folder, I'll make a D2 folder and put the rest in...