N64 emulation just kind of sucks, I guess?
You either can’t run or have major issues with:
Banjo-Tooie, Bomberman 64, Blast Corps, Donkey Kong 64, Excitebike 64, Jet Force Gemini, Mischief Makers, Mystical Ninja, Paper Mario, Perfect Dark, Majora’s Mask.
https://code.google.com/p/mupen64plus/wiki/GameCompatibility
Mupen64-libretro isn’t entirely the same as the standalone release as there have been some changes to the core, mostly for portability reasons. We actually have our own list, although it’s probably far from complete:
http://wiki.libretro.com/index.php?title=Nintendo_N64_Core_Compatibility
Nintendo 64 has always been in a terrible state. that’s no secret.
I played Majora’s Mask from beginning to end on a nightly a week ago without major issues. I got all the masks, but not all the heart pieces. I used Glide64 for graphics at 320x240 internal res. The most notable minor defects were: a few dungeon rooms lighting seemed messed up (looked like a disco), and a few stray fairies were invisible to the lens of truth (only knew they were there thanks to a walkthrough).
Have you tested many games on the core yourself? Some of the stuff in that list has definitely been fixed; I’ve run Blast Corps before and don’t really remember noticing anything major messed up in it. Seems like many of the issues listed are with Rice or glN64; Glide64 fixes a lot of stuff.
It’s far from accurate, but most games I’ve tried are quite playable.
Tested yesterday for well 20 minutes Donkey Kong 64 and Jet Force Gemini and had no issues.
I have also played flawlessly (first minutes too) Banjo-Tooie and Conquer’s Bad Fury before. I think things have been improved a lot lately thanks among other things to libretro.
Jet Force Gemini has 2 bugs: Grey character models appear on the upper left of the screen and there’s no shadow under the main character’s feet (same problem as Conker) I’m using nightly m64p core from 03/17/2015. You don’t have those issues? what core are you using?
Meant playability issues, I didn’t experience anything stated on the compatibility list. I also got some funky polygon stretching in DK64 once in a while, but as long as I tested it’s totally playable and doesn’t take you out from immersion or experience.