Final Burn Alpha Originally called the 'After Burner Emulator', Final Burn soon added support for other Sega games on similar hardware. In addition to those it has also started supporting CPS-2 games and a few of the CPS-1 games. Since the original Final Burn was discontinued by it's author (Dave), the Final Burn Alpha team have continued the project. Now available in Chinese too!
MAME (Multiple Arcade Machine Emulator) The biggest arcade emulator ever... need I say more? Also related is MESS which is the home console/computer version of MAME. Normal and i686 optimised versions available.
Tickle Tickle is an object oriented framework written to develop hardware emulators, but it can also used to write simple games and similar stuff. Tickle is composed by a portable library of functions and interfaces, and by an OS-dependent front end that provides access to system input and output devices (keyboard, mouse, joystick, sound, video and so on). The "Rebound" Edition contains a circuit emulator for Atari's Rebound (1973). It is far from complete and very CPU intensive but worth a look!