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Two d-pads, one analog stick, three triggers and two face buttons? What were they smoking in Kyoto in the early 90s 
I have only seen a Nintendo 64 in real life like twice back in the 90s so I have no clue what all these buttons do in most games.
Thanks to recent developments I went and downloaded every Nintendo emulator I could. I was surprised to see how fractured Nintendo 64 emulation seems to still be on PC. I was expecting there to be a Duckstation, PCSX2 or Dolphin equivalent but no, there seems to be no clear winner, and two of the bigger ones are closed source and use plugins like it's 2005, and one doesn't even come with a GUI by default
Here's how I'd map to like, a standard xbox controller:
Vanishingly few games use the L-trigger or the D-pad and the C-stick is pretty uncommon as well.
This is pretty good. If you were to add the emulator to steam as a non steam game and then launch the game from steam, you can have a few additional options too.
Like making the unused bumpers (or any unused buttons that might be available on the controller) a modifier key when it's held down which could let you map the other dpad to the same dpad.
Or you could make it so that a double click on the dpad becomes a click for the other dpad.
Also if you use the steam version of retroarch to emulate the game via steam (which is free) then you will find community provided layouts for the N64 controller for pretty much all the modern controllers.
Yup, this is how I use it. Left trigger is Z, Right trigger doesn't exist in N64 so it becomes a context button to turn ABXY into the appropriate C buttons. Right stick is also C for games where the C buttons work like a camera. Using the context button takes a bit of learning, but I like that this approach leaves buttons in roughly the same place (i.e. not mapping any face buttons to shoulders or triggers)