For SNES go with either Snes9x or the balanced bsnes core w/ RetroArch. Snes9x is pretty good all around, easy to use, good performance and very high compatiblity, but there may be a few glitches here or there. Balanced bsnes will play all (but 1 IIRC) games without glitches, but using higan can be a bit unuser-friendly so using RetroArch will bypass that - also has great shader support if you're into that kinda thing.
As for N64 it's kinda a mess, PJ64 is the most popular, but I've never liked it much myself, always ran into a bunch of annoying things. Been using Mupen64Plus recently and it's pretty nice, though it is command-line and has about the same compatibility as PJ64 and 1964. If you want the best experience and don't mind messing with multiple emus/plugins check this site for the game you want to play and follow its settings (it is using outdated builds though, but as not much has changed it's still pretty accurate):
http://bmgcl.atspace.cc/n64mgcl/N64ConfigList.htm
Also if you're interested in pure accuracy there is a cycle-accurate (like bsnes) N64 emulator in the works:
http://www.emutalk.net/threads/54131-Announcement-Cycle-accurate-N64-development-underway/
Its still got a ways to go before it's complete, and it'll require one helluva CPU to run though.
As for N64 it's kinda a mess, PJ64 is the most popular, but I've never liked it much myself, always ran into a bunch of annoying things. Been using Mupen64Plus recently and it's pretty nice, though it is command-line and has about the same compatibility as PJ64 and 1964. If you want the best experience and don't mind messing with multiple emus/plugins check this site for the game you want to play and follow its settings (it is using outdated builds though, but as not much has changed it's still pretty accurate):
http://bmgcl.atspace.cc/n64mgcl/N64ConfigList.htm
Also if you're interested in pure accuracy there is a cycle-accurate (like bsnes) N64 emulator in the works:
http://www.emutalk.net/threads/54131-Announcement-Cycle-accurate-N64-development-underway/
Its still got a ways to go before it's complete, and it'll require one helluva CPU to run though.