Citra - Citra is a work-in-progress emulator for the Nintendo 3DS.
TronDS - A Nintendo 3DS Emulator, It's very simple and is only capable of running homebrews.
RetroArch - RetroArch is a frontend for emulators, game engines and media players.
Drastic - Drastic is a Android DS Emulator
melonDS - A Nintendo DS emulator with support for commercial games.
DeSmuME - DeSmuME is a freeware emulator for the NDS roms & Nintendo DS Lite games created by YopYop156.