Well if no one else is gonna root for any other controllers, how about a couple non-portable ones (I like a beefy controller):
Logitech f310/f710. Good solid controllers, can be found lots of places (local and online), and they work with zero fuss (and have for a while). The analog triggers make good Z triggers in N64 games. The right analog usually substitutes for the C buttons.
PS3 controllers. Also easy to set up (auto-registers with bluetooth upon plugging in: no pairing needed). Also full-sized. Also available all over the place.
I also like that both have "unused" buttons (the PS/Logitech "guide" buttons) that make great hotkey buttons. It's a godsend in games that make heavy use of the select button.
The wired Logitech should never be over $20, and the other two can be had for $30-$40.
Don't get me wrong: the 8bitdo controllers are great. I just think that for N64/PS play, both original controllers had grip handles (to compensate for fingers manning the shoulder buttons more frequently), so using a controller with them helps. I find L2/R2 harder to use effectively on an NES30Pro.
If I was sticking primarily to the less shoulder-button/trigger-heavy games, I'd be all over a paddle-style controller like an 8bitdo.