Visual Boy Advance is definetely the best for GB Roms. I'd go with ZSNES. I really haven't tried the other SNES emulators, and I don't need to because ZSNES has given me 0 problems; and I've played quite a few games on it.
For N64 I would get both Project 64 and 1964. No N64 emulator is perfect as of yet, so if a rom doesn't work on Project 64, it should work fine on 1964 and vice versa.
And I will also recommend you use www.zophar.net