folders FTW, even better if you add custom badges for categories. There are also badge dividers

I use folders to organize my games by platform: Two for 3DS games, one for virtual console, one for mods, one for utilities such as system settings and camera, etc.

I organize Homebrew and Virtual Console on folders and the games in chronological order

Put your homebrew apps in a folder called "Homebrew" put your VC games in a folder called "Virtual Console" put DSi games in a folder called "DSi" put regular games in a folder called "Games" and put any other stuff in a folder called "Misc"

Who cares about organisation just look at the icons lmaoooooo