jGameBase - jGameBase is a fully-featured retro-gaming emulator frontend and game database utility.
Mesen - Mesen is a NES/Famicom emulator and NSF player.
Z26 - Z26 is one of the best emulators for the Atari 2600.
VirtuaNES - VirtuaNES is Famicom/NES emulator for Win32.
Javatari - Javatari is a multiplayer Atari 2600 emulator written in pure Java with no external libs.
Nestopia - A portable and cycle-accurate NES emulator written in C++