It's important to remember that current N64 emulation is absolutely horrible in every way imaginable.
Cen64 promises accurate low level emulation which will theoretically run everything perfectly. This also means PD will run at a glorious 3fps. (Emulator is still early WIP. Boots some games, though.)
Project64 1.6.1 is the go-to, combined with Glide64 Final. The emulator has some serious problems, but it's the best all round.
Project64 2.1 is a disaster which shouldn't be installed by anyone. For one, it has horribly broken timings, which breaks a long list of games. PJ64 is pretty much dead now, with one key dev jumping ship and the others doing other stuff.
Mupen64/Mupen64plus are decent, but obtuse. And Mupen64plus is plagued by a bunch of scene drama over plugin specs. Combined with a specific LLE RSP plugin, it is possible to run Indiana Jones and the Infernal Machine, though it is unstable.
1964 is a lot like PJ64. Differences aren't really that noteworthy.
The latest big thing to happen has been the GLideN64 plugin, which is a sort-of new HLE video plugin using OPENGL instead of Glide, which Glide64 used. While this plugin won't run the problematic Factor 5/BOSS games, and won't fix core emulation issues which break stuff like Mystical Ninja, (and cause EXPAND DONG) it will solve a fair few of the crippling performance and visual problems which plague N64 emulation. GLideN64 is due for public release in early 2015.
tl;dr: N64 emulation is awful, and many people who use N64 emulators have no clue just how broken everything is.