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N64 emulation is a complete mess. There are many good reasons for this, but they'd take too long to state. 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+Mupen64Plus, 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+ Mupen64Plus 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.
*RetroArch has incorporated a heavily modified fork of Mupen64+ Mupen64Plus as its N64 core, it is still a WIP and may have issues but should be fine for most games now. It is constantly being worked on, and has features not present in mainline, such as Project64-style overclocking for faster framerates and 3-point texture filtering, as well as those features that RetroArch itself brings.
*Bizhawk has a port of M64+Mupen64Plus, which seems to work well enough. Bizhawk lacks portability however, and is only for Windows and OSX.
*Daedalus is an N64 emulator for the PSP, which has been ported to Windows, but results are even more hit-and-miss than on other emulators due to being made for PSP first and foremost. On PSP, most games are unplayable, but there's a [http://forums.daedalusx64.com/compat.php small amount of them that work really well] with the right settings (Quest 64, for example).
