For the native emulators (and any additional native emus), all that really matters is the location of our roms right?
I personally have my "3D game" renamed to "Apps" and "Interesting game" renamed to "Roms"
Under "Roms" I have a folder for each system, and then if there are lots of games, folders for groups of letters (e.g. "A-F", "G-L", "M-R", etc)
As the "Apps" and "Roms" menu items look in the same place, this would probably cause a problem if you decided to categorise any native homebrew in a similar way, because for each category you would see seemingly empty directories for files from the other (as the "Roms" can't see .app files, and "Apps" can't see roms)
Just something to consider