1. The Legend of Zelda: Majora's Mask ; Not only did Majora's Mask have the near impossible task of following up to Ocarina of Time, but it was released near the end of the Nintendo 64 lifecycle when most consumers were looking towards the next generation of systems. Despite all the forces against it, Nintendo somehow managed to pull off one of the most unique and engaging games of all time by doing something completely different than its predecessor. Majora's Mask creates a setting that is so dark and so fascinating it's hard to not get sucked in emotionally. Watching the people of Termina is both mesmerizing and depressing as you watch them all react to their impending demise as the world is crashing in around them. The blend of amazing Zelda style gameplay paired with tremendous side characters, stories, and quests creates one of the most amazing game experiences of all time. No game has ever replicated what was achieved in Majora's Mask and not only does it stand as the greatest Nintendo game of all time, but likely THE greatest game of all time. It simply cannot be overlooked.
2. Pokemon Gold / Silver / Crystal ; It's hard to narrow down a specific entry within the Pokemon series as "the best" as the most recent iteration has always perfected many nuances and mistakes from previous generations. However Generation 2 on Game Boy Color is in my opinion the point where Nintendo had shown that Pokemon was not just a one hit wonder, it was a powerhouse to come. With 251 monsters, two regions to explore, backwards compatibility, and completely revamped graphics/animations ALL WITH COLOR was completely mind blowing back in the day. Yes the game has its issues, but to me Pokemon Gold/Silver/Crystal managed to capture what made the originals so great but also put in the stepping stones for what the series would become and how complex this "kids" game really was. From breeding, to genders, to shinies, there was a lot of thought and craft put into these games. It's also just fun as hell in the most simple way possible.
3. Super Mario World ; The Mario series exists in two forms, one being 2D and the other in 3D. While there are similarities among them, I believe it's difficult to compare them directly due to the constraints or limitations between each games movement and gameplay style. However as a collective if I had to pick one Mario title to play for the rest of my life, Super Mario World would be it. Learning from its NES predecessors, Super Mario World exploded onto the Super Nintendo day one with everything that made the original trilogy so great with its own flare and fun. A ridiculous amount of levels remains constantly fun through setting variety, unique gameplay situations (lava runs, flying levels, balloons, etc.) and fun characters (Yoshi!) and enemies (Koopa Kids!). It's run and jump gaming at its most pure and fun form. I still discover secrets now and again when playing nearly 30 years later.
4. Banjo-Kazooie ; Oddly this in my opinion is the greatest 3D Mario game ever created. Despite the unique attributes of the game, a lot of what Banjo-Kazooie does so well at can clearly be traced back to what was first introduced in Super Mario 64. But that's the beauty of Banjo-Kazooie as despite Super Mario 64's amazing gameplay, it had its flaws, and Banjo-Kazooie created an overall better experience. The comedy, the characters, the bright surroundings, the tight and varied controls all make this game an absolute memorable experience. While the series has lost its way over the years, Banjo-Kazooie kept itself simple in the original entry and did not get bogged down by multiplayer and overly complex level design (Tooie) or gimmicky gameplay (Nuts and Bolts). A lot of games from the Nintendo 64 have not been able to stand the test of time, but this game absolutely has.
5. Conker's Bad Fur Day ; Does this game count? I sure as hell hope so. This game was so controversial for Nintendo that they didn't even publish it in fear of what it would due to their image. Similarly to what was done in Majora's Mask, Conker's Bad Fur Day is a game that really has never been replicated over the years. Sure it's a platformer, but it's also a lot more than that. Third person shooter, self aware satire, cultural influences to gameplay, dirty toilet humor, and shockingly great multiplayer. Conker's Bad Fur Day was the best example to show how truly varied Rare was at game creation in that they had the balls to create the anti-thesis to a platform title in an age where we were drowning in them and still pull off one of the greatest games ever made. This game is a fucking ride from the moment it starts.
6. Animal Crossing ; Another series that is hard to pinpoint an entry given that odds are the most recent entry is likely the best given its tweaks to the formula, but I'm a sucker for originals. Animal Crossing on the original GameCube was such an odd experience when I first played it. It was hard to explain what made it so fascinating and fun. I told friends you live in a town and run errands, collect things, and build your house. That's really all there is to it. Yet its somehow extremely addicting. And relaxing. I have so many memories as a teenager strolling through my town in the middle of the night and just listening to the calming music and interacting with the animals who for whatever reason were still outside and not sleeping. It's a calming game with no set objective, just simple fun. While I would recommend Wild World or New Leaf to any new entrant to the series, I have to give props to Nintendo for what they were able to accomplish on the original home console version.
7. Super Smash Bros. Melee ; What's there to say really about this game that probably hasn't already been said by everyone? The sheer amount of content of this game is mind-blowing at the time and is the best example of how rich and deep Nintendo's history and catalogue of characters and stories really is. Part of the beauty of this game was the release when the internet was still in its infancy. Character leaks really didn't exist, and the roster, levels, trophies and items was astonishing as a kid who had never been exposed to a lot of Nintendo's archives at the time. Local multiplayer has sadly started dying off over the years, but there's something about Super Smash Bros. Melee that has the ability to bring a room together. So damn fun.
8. The Legend of Zelda: Link's Awakening ; To me the best Zelda games are the ones that don't follow the same familiar formula that was put in place by A Link to the Past, and a lot fall into the trap in trying to replicate. Majora's Mask does it the best, but Link's Awakening is a close second. There's no Ganon. No Zelda. Really, no familiar faces at all. You find yourself in a bizarre world that is overrun with monsters and needs a hero to delve into what really is behind this crazy setting. The dream state environment and emotional story is absolutely shocking given the primitive hardware that this game was released on. It's 2D Zelda at the top of its game and blows away action/adventure games that are released even to this day. I wish the Zelda team would take more inspirations from this title, but sadly it's often overlooked throughout the history of the series.
9. Paper Mario: The Thousand Year Door ; It's so depressing to see that Nintendo and Intelligent Systems have been floundering with the Paper Mario series over the years given this entry is by far one of the greatest RPG's of all time. The gameplay is simple which can be a turnover to some more hardcore RPG fanatics, but the atmosphere, visuals, music, and story telling are some of the best in the genre. Mario & Luigi series is fun, but what is great about Paper Mario is the variety in characters that can be implanted into your party and how they impact the overall landscape of the game. Every character in this game both playable and non-playable is interesting and fun to talk to which is madness given the level of characters scattered throughout the land. One day I hope we get a true successor to this title.
10. Mario Golf: Advance Tour ; I'm probably an odd one out on this title, but there's something about Nintendo golf games that create an experience like any other sporting title. The mix of RPG elements and arcade style gaming is Advance Tour make it by far one of the best portable experiences out there. The unique Camelot characters are a bit odd, but building their stats and importing them into the GameCube version gives even more content to this already overloaded title. This game probably spent the most amount of time loaded into my Game Boy Micro and saved me a lot of headaches as played in secrecy at my desk in high school. The recent 3DS title was a dud, wish they could come back to their roots with this one.
Honorable Mentions
xx. Super Mario 64
xx. Pokemon X/Y
xx. Super Mario Galaxy
xx. New Super Mario Bros. U
xx. Kirby's Air Ride
xx. Mario Kart 64
xx. Super Mario Land 2: Six Golden Coins
xx. Super Mario Land 3: Wario Land
xx. Kirby's Dreamcourse
xx. Kirby's Pinball
xx. Pokemon Pinball R/S
xx. Metroid Pinball
xx. The Legend of Zelda: Oracle of Seasons