The 2.0.0.1 version bundled with Project64 2.1 may have some regressions, however, so Glide64 Final may be worth keeping around just in case. Still, it is overall the best plugin for general use. Often much more accurate and compatible than Jabo's plugin, and has a wealth of options, though it can be slower on lower end machines, and may not work on integrated graphics.
Sadly, it will likely never see another update again.
The most recent version included with Project64 2.x (1.7.0.57-ver5) is somewhat buggy and has regressions, however, so the version included in Jabo's 1.6.1 patch is recommended instead for most cases, though the former can run in LLE mode, which can help with a few games. Very speedy, can potentially look the prettiest due to built-in AA and AF options, and is the only plugin with a widescreen hack.
It also fixed a number of games that were completely broken in 1.6, such as Kirby 64. However, the user interface is quite a bit nicer and easier to use, and switching between RSP plugins is far easier than in 1.6.
Some users have also reported problems with BSODs, which apparently may be an issue with outdated Windows system files. Its RDB is somewhat outdated, and some games have issues with audio and timing regardless of plugin setup unless you mess around with timing settings.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).