Wow, I'm gonna shoot myself if I see another "What is the best" thread. I wish people would start making posts asking "What is your favorite game" or "Name your top 10 favorite bands". The world is rarely so black and white where a unanimous decision on the best of anything can be made. Rarely there is a best, there are usually a series of pros and cons that you have to weigh and decide which is more important to you. Is the story in Ocarina of time better than the gameplay of Mario 64? Maybe, maybe not. Is the super fast response time in your LCD better than the colour reproduction in someone elses?
I think it's perfectly valid to find out what other people like and then you can see if there is one or two things coming up a lot and check it out if you haven't already. The best is what you strive for but can rarely attain.
With that said, my favorite emulated games are:
Zelda: Ocarina of Time
Mario 64
Banjo Kazooie
Banjo Tooie
Conker's Bad Fur Day
Blast Corps
Probably some more I can't think of right now <- this isn't actually an N64 title
If you are looking for a game that is emulated the best (compatibility wise) you'll probably get a list with Mario 64 and Zelda on it but even that is hard to pinpoint.