It's rather hard to choose a single game for each...
N64: Super Mario 64, Blast Corps
SNES: Final Fantasy IV, Final Fantasy VI, Chrono Trigger, Link to the Past, Super Metroid, Star Fox, Super Mario World, Killer Instinct, Super Street Fighter II, Mega Man X, Mario Kart
NES: Super Mario Bros, Super Mario Bros 3, Mega Man 1+, Duck Hunt
Part of that is mostly just the games that I remember the most, but they may not be the best. For example, I remember having trouble timing out seconds to properly execute moves in Street Fighter, and my dad ended up giving me a helpful tip to do it properly. From then on, I could Sonic Boom with the best of them! It's also worthwhile to consider that I haven't played a lot of the second half of the N64's library, because my brother and I sold our N64 to buy a PlayStation.