I hear mupen64 plus is a good one, but I wasn't able to get it to run myself.
I would love to play some Excitebike 64, WaveRace, Mischief Makers and others, but even though I still own the games and console, I don't have a single N64 controller whose analog stick isn't completely busted. Far as I'm considered, those fucking controllers were a bigger pissoff than the Virtual Boy.