Even though its last update by its original author was in 2005, it is possibly even more compatible than Project64, particularly with more obscure or less discussed titles, though it has incompatibilities of its own. Mupen64 - An open source, multiplatform N64 emulator.
Overall, it is the least compatible of the big three emulators, only being useful for a handful of games. It is generally recommended to stick to version 1.1 except on certain special cases. The last stable version released by the original team was 1.1, who then went on to remake it as a web emulator written in JavaScript, though some community members kept it going up to version 1.2 r146, with mixed results. Some of its iterations (such as 1964 Ultrafast) have the ability to overclock the N64's CPU, which results in smoother framerate on games that have a lot of slowdown, such as Perfect Dark and Conker's Bad Fur Day.
Some users have also reported problems with BSODs, which apparently may be an issue with outdated Windows system files. Its RDB is somewhat outdated, and some games have issues with audio and timing regardless of plugin setup unless you mess around with timing settings.
Project64 2.3 - The most recent version of Project64, now public and open source (though the official download asks you to install useless toolbars).