The Emulation Station
(Use Retroarch when possible)

Retroarch (Game emulator)    [Alternate version]     [alt2]

N64 Wasm (N64 Emulator)

WasmBoy   (Gameboy emulator #1) 

VaporBoy (Gameboy emulator #2) 

SkyEmu (Gameboy emulator #3) 

PinkyNES (NES emulator)

Desmond (DS emulator, not recommended over Retroarch)

ScummVM (Pajama sam, Monkey Island, stuff like that)

Tiny8Bit (Collection of 8-bit computer emulators, with games)