Mupen64Plus - N64 emulator and plugins for Linux, Mac OSX, FreeBSD, and Windows
Citra - Citra is a work-in-progress emulator for the Nintendo 3DS.
Project64 - Project64 is a Nintendo 64 emulator for the Windows platform.
3dmoo - 3DS Emulator Prototype
RetroArch - RetroArch is a frontend for emulators, game engines and media players.
Corn - Corn is a very fast Nintendo 64 emulator.