Ones I have personally used and endorse (will play most games at full speed with sufficient hardware) will be marked by an * (asterisk). For more emulators and systems go to: my main thread
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*Project64: This one is a great emulator with great compatibility. 1.6 was the last public release in 2005; 1.7 has been in 'beta' since then with access to 'donators'. Update: they have moved out of beta stage, and 2.0 was released to the public, followed shortly by 2.1.
*Project64k: adds Kaillera (netplay) to Project64.
-Project64K7E: an alternative to Project64k.
*Mupen64: a good emulator with great compatibility. No longer maintained as of 2005.
*Mupen64k: adds Kaillera (netplay) to Mupen64
*Mupen64Plus: While the original Mupen64 is no longer being developed, this branch is a continuation of the project, with support for more systems, although the Windows version only offers an official 32bit binary.
*1964: a nice choice for good compatibility with most games.
-ICE64: an unofficial split from the 1964 1.1 source. Made by Pokefan, this emulator has went through many name changes in it's lifetime, including ICE64, NICE64, and STX64 (he allegedly changes the name whenever he is under pressure to release the source code) and as far as I can tell, it is not supported any longer under any known name.
-NICE64: See ICE64 above.