Mine would have to be like this top-5 list:
1. Banjo-Tooie. It took all the elements of the original and expanded on them. Example, first-person shooter sections being an expansion of egg-shooting, underwater shooting, splitting up, these were great expansions of the Banjo-Kazooie recipe. The levels and puzzles were, again, great and pretty intuitive, there were great boss fights and the fight with the witch is, of course, intense. Like Banjo-Kazooie, there's no penalty/bad ending for cheating, so that's always good. Plus the commercial was hilarious (Banjo goes skydiving, expecting Kazooie to be in his backpack, he finds out she's not, lands flat on his face while Kazooie watches from a lawn chair. Did I mention it's people in costumes?).
2. Super Mario 64. I don't know what it is, but Nintendo has a really asinine way of naming games. Super Nintendo, it was "Super" everything. N64, it was "Name 64". Anyway. Super Mario 64 is how you do a 3D platformer, just like how the original Super Mario Brothers games were how you do 2D platforming. I rate this higher than Legend of Zelda: Ocarina of Time because it introduced new elements of gameplay like the Feather, Metal and Specter (I don't know what it's called) Hats, the level design was out of control and the fights with Bowser were always great and challenging. Personally I loved Rainbow Ride.
3. Banjo-Kazoooie. Yeah, the original and the sequel are both on the list. Yeah, they both deserve it. Considering he's one of the only two Diddy Kong Racing characters to have a career after DKR (the other being Conker...scary thought), it's pretty shocking. The game is basically a scavenger hunt, but I love how it was presented, lots of interesting puzzles and levels (even if there is the usual suspects like a water-themed world), and unlike in most games, every ability had a use. That's pretty unprescedented. Plus, fighting Gruntilda the witch was at first hilarious, then intense. And unlike in this day and age, you're not penalized for cheating! Well not from the game anyway...
4. Harvest Moon 64. I know what you're going to say, "Harvest Moon 64, the farming sim?!" Yeah, I know, it's a guilty pleasure and it defines "sleeper hit" because it has a very sleepy, slow pace that's a good contrast to today's fast-paced, hot-blooded, adrenaline-fueled games. It's a nice, quiet game. There's nothing to kill, nobody to save, it's just you, your dog, a farm and a town full of people to interact and become friends with. It's a good contrast to today's over-the-top action games, in that sometimes it's nice to just slow down the pace and breathe. Time moves a little too fast in the game, though, that's my only knock against it. But it's not that bad once you get into a groove.
5. 007 Goldeneye/Perfect Dark. Both are pretty much the defining shooters for the N64, and both are how you're supposed to make a shooter. Goldeneye is the pinnacle of FPS multiplayer, and Perfect Dark is how to make an FPS with a great story, even if it does include aliens. And Rare again did FPS storytelling right in Perfect Dark: Zero, even if the gameplay and environments were kinda bland. Plus, Goldeneye did something else right: made a good movie tie-in game (!!) that was still fun years later. Goldeneye, as a movie, doesn't have nearly the staying power that Goldeneye the game does. As far as Bond's other movies go, it's certainly not one of his more memorable ones. The game, however, is a great and one of the defining N64 shooters, especially in multiplayer mode. It's fun to play, great with friends and my favorite thing about it is that it's local so you can kick someone's ass for picking Oddjob in multiplayer. Fucking cheap little hat-throwing bastard...
Honorable Mention: Super Smash Bros. To be honest, this one missed the top five because I think the formula was perefected in the second game, Super Smash Bros. Melee, but the first one has its moments.
Honorable Mention: Legend of Zelda: Ocarina of Time/Majora's Mask. Why is this an Honorable Mention? Well it did show how to do 3D Zelda and it didn't deviate from the storyline of Zelda (Zelda gets in pickle, Link un-pickles her), so why is it so low? In truth, I put it here because it didn't really add any new elements into the Zelda world other than a new dimension. Mario 64 did add new elements, Legend of Zelda has been following the same formula since Zelda I: Go to dungeon, get item, kill boss, rinse, repeat. That said, Ocarina of Time and Majora's Mask are both great games, and deserve to be in any 64 fan's library.
Honorable Mention: Rush 2: Extreme Racing USA. This was a racer title and the follow-up to the arcade speed-fest, San Franciso Rush: Extreme Racing. Though technically a multi-platform title (it was released on the Playstation and might've been on Sega Saturn), I thought the 64 version was the best racer on the system. It had all the speed and insane jumps that made Rush such a blast, it had some of the coolest courses I've ever seen in a game (ever race through Hawaii and get across the water by jumping from aircraft carrier to aircraft carrier or race through the New York City subway and drive up the wall to avoid a subway car?) and a great soundtrack. And of course, the cars were great, too. There were no brand-name cars, just things like "Van," "Sedan," "Muscle Car," and "Prototype". Proving that you don't need an expensive license to make a great speed-fueled ride, here's to you, Rush 2. Now come back to us. With the improved graphics of today, we'd love to have a new-age Rush on the consoles in contrast to the shitfest that is Need For Speed!