higan is a multi-system emulator that is known for emulating its underlying hardware very accurately. It can run every SNES title ever released. It started as a SNES emulator but currently supports over 10 systems.
Mednafen is a portable, utilizing OpenGL and SDL, argument(command-line)-driven multi-system emulator.
MAME is a multi-purpose emulation framework.
MAME's purpose is to preserve decades of software history. As electronic technology continues to rush forward, MAME prevents this important "vintage" software from being lost and forgotten. This is achieved by documenting the hardware and how it functions. The source code to MAME serves as this documentation. The fact that the software is usable serves primarily to validate the accuracy of the documentation (how else can you prove that you have recreated the hardware faithfully?). Over time, MAME (originally stood for Multiple Arcade Machine Emulator) absorbed the sister-project MESS (Multi Emulator Super System), so MAME now documents a wide variety of (mostly vintage) computers, video game consoles and calculators, in addition to the arcade video games that were its initial focus.
Kega Fusion, also shortened as Fusion and initially named Kega II, is a multi-system emulator for Windows, Linux and Mac OS X developed by Steve Snake. It is the follow-up to Kega Lazarus, and is the last in Steve Snake's Sega emulators after KGen, KGen98, Kega and Lazarus.