The C= 64's SID chip in is a pretty cool and complex digital and analog device...
I'm sure its difficult to emulate...
As far as emulators, I really have only run ShapeShifter and PC-Task. Shapeshifter runs most games great except for Sierra. Never been able to get any of those working.
Which Nintendo emulator are you using? I did try one and I thought it ran sort of choppy hard to play Super Mario and I have an 060. I don't recall which one I was running... Maybe I was not using the best one...