Super Mario Sunshine
As much as I love Galaxy, because Super Mario is a platforming series, Sunshine beats it out by having bigger continuous worlds to explore and better-feeling controls. Sunshine feels great and looks great and is so much fun to run around in - is there anything more satisfying than jumping over boats around Delfino Plaza with the Turbo Nozzle on? No, there isn't. I absolutely love its island vacation vibe and it's so much fun to play around in.
A game that feels like Sunshine and looks/sounds like Galaxy would be effectively the perfect Mario game. ...I should play Odyssey sometime, huh?
Paper Mario: The Thousand-Year Door
This game took the "paper" theme from 64 and turned it into a whole unified aesthetic. It looks fantastic and the added mechanics (like the "reflect" guard, and the AUDIENCES!!) were so interesting. This is what people want when they ask for a sequel: something that takes the original ideas and runs with them in interesting directions.
My sole complaint about TTYD is, by nature of its foreground-background distinction, the levels feel way too left-right oriented, which takes me out of it somewhat and makes it a little less fun to explore. At that point you might as well make a platformer, and if I am playing a Paper Mario platformer... well, let's say there's another one I'd rather be playing.
That said, this game is beloved for a reason. Glitz Pit and Excess Express are absolute highlights of the entire series.
Professor Layton and the Curious Village
Along the same vein as Ace Attorney, I'm only mentioning the real knockout entries for Professor Layton that I have disproportionately strong opinions on.
I played Professor Layton and the Curious Village shortly after I had been introduced to Detective Conan, and these two factors are equally responsible for the birth of my obsession with anime detectives. Curious Village was formative. Who in the Hell wants to watch RDJ Sherlock Holmes which is just a mediocre action movie with Jude Law as its sole redeeming feature, when you can instead solve puzzles to a fantastically serene soundtrack and then the villain remote controls a ferris wheel to try and run you over.
Professor Layton and the Curious Village captivated me with its pleasant atmosphere, its fun and cute completely pointless minigames, puzzles that made me feel smart when I solved them, and an absolutely ridiculous story. I'm sure if I were playing it for the first time now I might not think so highly of it, but it was the first thing of its ilk I'd ever experienced at the time, and I fell in love.
The meditative nature of the puzzle BGM is almost magical. I love every composition like it in the series.
The Legend of Zelda: Majora's Mask 3D (Project Restoration ver.)
There is so much for me to say here and I don't trust myself to do any of it justice. So I'll say this: Majora's Mask was my favorite Zelda game for a very long time, and one of my favorite games period. As an adult I find myself unable to get the same magic from the 64 version that I once did, and I'm endlessly frustrated by a lot of changes made in the 3DS version. But the "Project Restoration" patch (which requires homebrew to install) removes the majority of these frustrations, and creates a version of Majora's Mask I am once again able to play and enjoy. It's beautiful and unique and fun and just so unlike any other Zelda game, in a way that will absolutely always be special.
The Legend of Zelda: Twilight Princess
The only part of Twilight Princess I don't love is its ending, but fortunately, it's not a mystery game, so the ending pretty much doesn't matter and I can largely ignore it.
Twilight Princess is the most aesthetic Zelda game. I stand by this and dare Nintendo to disprove this stance in any future installments. I am also a huge fan of werewolves, and this game is literally everything a werewolf fan and OoT-era Zelda fan could want. Wolf Link's design slaps hard.
The visual that comes to my mind when I think of Twilight Princess, though, isn't Wolf Link or the twilight realm or any of that. It's me (Link) standing on a ledge somewhere on Hyrule Field where I'd just murdered a Poe, looking up at the moon in the starry sky, hearing Epona making horse noises faintly below me, and just... pausing, for a bit.
Twilight Princess's overworld was fun to explore, and in that moment, I really felt like someone on an adventure, a person and my horse, spending the night camping in a nook before setting off again the next morning.
Lost Woods and Hyrule Castle have such indescribably wonderful atmospheres. Twilight Princess excels at atmosphere and it's what makes it such a strong entry all these years later.
(Plus you can play FETCH with the DOGGIES and PICK THEM UP!!!!!)
Super Smash Bros. Brawl
Subspace Emissary is literally the trigger that got me to play the MOTHER series. It is the only work deserving of the title "Most Ambitious Crossover of All Time". You could call Ultimate that, but Ultimate is too cowardly to have a good single-player story/adventure mode, so it's not much of a crossover now is it? Samus liberates Pikachu from enslavement. Sonic the Hedgehog saves everyone at the end in a scene that can only be described as a "my uncle works at Nintendo"-tier moment, but actually true. Friendship Ended with every single post-Brawl Smash game. If all they do is fight it's boring and I don't care.
I have 3DS now and I will try that one out, but I'm not holding my breath.
Super Smas Bros. Melee
Melee's Adventure mode may not be Subspace Emissary, but it's still so much fun. Oh, the hours spent running through it over and over as the same characters for no reason than because it was fun. Platforming in the Smash engine is just so much fun, it's a great way to learn the characters and makes it a game to come back to, not just something to play when friends are over.
Melee feels a little better than Brawl does, and I played it a lot more, so it's more important to me. Both are very dear.
Donkey Kong Country: Tropical Freeze
I played this game couch co-op with a friend when I was waiting for my car to be ready for repairs. Compared to growing up with siblings, I have significantly fewer opportunities to play couch co-op as an adult, so that was a really special and really fun experience. It's such a fantastic multiplayer game. I treasure this memory, even if it was just for a couple hours a few years ago.
This was also one of the defining games that informed my decision to further my music education. I had been listening to the Donkey Kong Country 2 soundtrack for more or less my whole life, and it's absolutely phenomenal and I still love it immensely. But... listening to what David Wise produced, in the modern era where technology is no longer a limiting factor... it changed my entire perspective. This is by no means to undersell what he was able to create on the SNES, because that was also life-changing. But Tropical Freeze made me realize that one of my biggest inspirations as a musician, has for the past couple decades, been constantly growing and learning new technologies. And if I want to make music like that someday, I need to also grow, and learn new technologies.
Paper Mario 64
DZ really hit the nail on the head with this one when they described this game as cozy, because that's really what it is. This game is so comfortable. I love the little distinctive character themes that fade in and out when you wander around Toad Town, and all the different designs of the Toads who inhabit it. I loved drawing little Toad-sonas in my notebooks at school, I loved hanging out in little nooks (chilling with Moustafa on rooftops, hanging with that one Koopa with the radio in his house...), it is just such a charming and cute game and I love it so much. The Peach espionage segments are so much fun too, second only to the Bowser levels in TTYD which were absolute top shelf quality.
I love how it just feels like a storybook and aesthetically mimics an arts-and-crafts project. Its highest highs don't match Glitz Pit or Excess Express, but overall its feel just speaks to me so much more than TTYD, hence their relative positions.
I think Sonic Adventure's approach to storytelling - by showing the same narrative from different perspectives, exploring some of the same levels and some different, was super cool. The implementation is kind of extremely awkward in that Tails's levels are just Sonic's levels but a joke now because his flight is broken and you just yeet over the whole thing, but it's fun so who cares. I don't play Sonic for the level design. I play Sonic so sick jams can play in the background while a cheesy story starring anthropomorphic hedgehogs plays out. No more and no less.
Adventure is much higher than Adventure 2: Battle because I really like hub worlds. I think dicking around in Station Square is my favorite thing about Sonic Adventure, because you can cause traffic jams, and carry around that one statue of the guy who looks exactly like that other guy who isn't a statue but is in fact a guy. Also, you can play as Tails outside of his mech, and you can play as Amy. Two things SA2B was missing. I played Sonic Adventure after I played its sequel, but I came to love it more.