For organization.
Folder for system/firmware files
Folder for DS games
Folder for NES / GBC / SNES games
Folder for homebrew
Folder for music
Folder for movies
Folder for eBooks
Typically anything else is hidden.
Since your system/firmware folder is typically hidden, the average person (who uses folders) is left with about 4~6 folders each of them being organized into their category for easy browsing.