Calice32 This is by the author of BeGameboy and BePCEngine. It emulates Capcom CPS-1 and CPS-2 games plus the QSound from ZN-1 and ZN-2 games. It also emulates some of Sega's System-16 based games. The original DOS port is no longer supported.
GNGEO A Neo-Geo emulator for Linux. Sorry but I can't list the games that are supported here in CAESAR. It would be a huge amount of work to work out the required ROMs without CRC information in the emulator and I don't have Linux to do proper testing either!
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.