Pretty much any controller is supported, I have a wireless PS3 style controller and a wired PS3 real controller and both are detected and work perfectly with everything I use
Some games may be a bit awkward to play without specific controllers, but if you can get an N64 controller there are people that use specific controllers for specific systems and one just for everything else
Not all N64 games work, but the vast majoirt do. I have N64 games, but only those they are verified and tested working 100%
This is an outdated list now, but wil give you a good idea to what is possible on the PI3 N64. Quite a lot does work though, mainly concentrating on the popular games for 100% compatibility and support
https://wiki.gbatemp.net/wiki/Wii64_Compatibility_List
Wii/GameCube is really a "proof of concept". It will work, but so incredible sluggish and terrible it really isn't work trying (and probably never will) on the PI hardware. 3DO and SEGA Saturn emulation is also possible and supported. They WILL work but just not quick enough to actually be usable