Just an idea at the moment, I'd probably port ZSNES over to the N64 with some hacks for speed. I think it might be possible to achieve some reasonable performance, using many hardware tricks (like parallel processing and maybe the RDP, if I can ever figure out how to use it.)
But don't expect me to even start it until the next Neon64 is released.
(By the way, though it may appear on the front page that this is a joke, I really am considering this project.)