Emulation/On PC - Linux

Arcade

 * MAME

NES

 * FakeNES
 * FCE Ultra

SNES

 * Snes9x
 * ZSNES

Nintendo 64

 * Mupen64

Playstation

 * EPSXe
 * PCSX
 * pSX

Playstation 2

 * PCSX2

Gameboy and Gameboy Color

 * KiGB
 * GNGB
 * Gnuboy
 * VisualBoyAdvance
 * RealBoy

Gameboy and Gameboy Color and Gameboy Advance

 * VGBA (Virtual Gameboy Advance)
 * VisualBoyAdvance
 * EmulationStation

DOS

 * Dosbox

Windows

 * Wine (not a true emulator)
 * VirtualBox

See also Ubuntu (Linux) Guide/Virtualization for other ways to emulate Windows on a Linux PC.