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In terms of compatibility with the N64's game library, vanilla Mupen64 was basically on par with if not superior to Project64 1.6, with 1964 lagging quite a bit behind the two. Mupen64Plus improves upon Mupen64 even further, while Project64 2.1 [http://forum.pj64-emu.com/showthread.php?t=3601 only fixed a few things and broke others]. Mupen64Plus is receiving far more updates, and will likely be the go-to emulator for general use in the future.
→Comparisons
N64 emulation is a complete mess. Every emulator has its own unique compatibility issues, and it varies significantly even within one emulator if using different plugins. Refer to [http://bmgcl.atspace.cc/n64mgcl/N64ConfigList.htm this link] for optimal emulator settings based on the game you want to play.
*Mupen64+, based on Hacktarux's Mupen64, is currently the best overall N64 emulator, but you still need PJ64 for certain games. It lacks a native GUI, and instead is ran by dragging and dropping roms and editing the config with Notepad++. There are third-party GUIs made for it, but many are problematic and glitchy. It is actively developed, and has been ported to a number of different platforms.
*Project64 is still a decent choice for emulating most of the popular games, though it has been supplanted by Mupen64+ in terms of general compatibility. It is capable of using a wide variety of plugins, and has a relatively user-friendly interface. However, it has not seen an update in some time, and remains confined to Windows. Version 2.1 fixed some games, but introduced some regressions as well, so it may be handy to keep version 1.6 alongside it.
