Multi System

DarcNES
An open source emulator for AmigaOS, BeOS, BSD, DOS, Linux and Windows. Supports the Apple 2, ColecoVision, Game Gear, Master System, MSX, NES, PCE/TGX, SC-3000, and SG-1000.
http://www.dridus.com/~nyef/darcnes/

Emulator 3000
A freeware emulator for Windows. Supports various Russian and foreign computers including Agat-9, Bashkiria-2M, Elektronika BK-0010*, Mikrosha, Partner 01.01, Pyldin-601*, Vector-06C, and ZX Spectrum.
http://www.emulator3000.emuita.it/e3.htm

FreezeSMS
A freeware emulator for Windows. Support ColecoVision, Game Gear, Master System, NES and SG-1000.
http://freezesms.emuunlim.com/

Mednafen
An open source Game Boy, Lynx, NES, PC Engine, SuperGrafx, Neo Geo Pocket, PC-FX, and WonderSwan emulator for Linux and Windows.
http://sourceforge.net/projects/mednafen/

MEKA
A freeware emulator for DOS, Linux/i386, and Windows. Supports ColecoVision, Game Gear, Master System, Othello Multivision, SC-3000, Sega Mark III, and SG-1000.
http://www.smspower.org/meka/

Xe
A freeware emulator for Linux/i386, Linux/PPC, and Windows requiring GTK+2.0. Supports CPS Changer, Game Boy, Game Gear, Master System, Mega Drive / Genesis, Neo Geo, Neo Geo Pocket, NES, SG-1000, Super NES, Turbo Grafx16, Turbo Grafx CD, and WonderSwan.
http://www.xe-emulator.com/