Citra - Citra is a work-in-progress emulator for the Nintendo 3DS.
RetroArch - RetroArch is a frontend for emulators, game engines and media players.
3dmoo - 3DS Emulator Prototype
Snes9x - Snes9x is a portable, Super Nintendo Entertainment System (SNES) emulator.
BSNES - bsnes is a Super Nintendo (SNES) emulator focused on performance, features, and ease of use.
TronDS - A Nintendo 3DS Emulator, It's very simple and is only capable of running homebrews.