Super Metroid (SNES)
Castlevania: Symphony of the Night (PSX) It introduced us to the "Metroid" style of playing and exploring that we all know and love.
Contra Hard Corps (Genesis)
Sonic the Hedgehog 3 & Knuckles (Genesis) Technically two games but it was meant to be one cohesive adventure. So I'm putting it here.
Super Mario Sunshine (GC) One of(if not, THE) best 3D Mario games out there!
Silent Hills 1-3 (PSX, PS2, etc.) The original trilogy of the SH games are all masterpieces in my opinion. Gotta love psychological horror!
Resident Evil (GC) The Gamecube remake of the original RE is what got me into the RE series in the first place and also, survival horror in general.
Undertale (PC)
Probably some more I'm forgetting but will add as I remember!
Mother 3 (being my personal favourite) is pretty well crafted in all regards. Music, Story and Visuals are all expertly done. Better yet is that the vision of the game is pretty well documented so it'd be very hard to argue it didn't do everything it tried to do. Just a real great game all around, so I see no reason not to call it a masterpiece.
If I was to pick a singular game that I would consider a masterpiece though, I'd have to say Xenoblade Chronicles. The sheer feeling of adventure that oozes from that game is phenomenal. Even if you dislike a character to begin with, chances are you'll be dreading saying goodbye to them by the end. There's so much emotion and wonder packed into the game, it can feel epic and relaxing all at the same time and it's just plain beautiful. As much as I enjoyed Xenoblade X and am looking forward to 2, I think it would be exceedingly difficult to match this game, let alone surpass it.
The paper mario series (before sticker star). Mario and luigi: Bowsers Inside story, BOTW, Undertale, Mother 3, Earthbound, Snake Pass, Minecraft, Smash bros brawl.
The Last of Us.
I think that's the only game I've played that I truly consider a masterpiece.
Maybe Silent Hill 2. I can only imagine how wild it would've been if I hadn't been spoiled for the twist. Even knowing it, it was a fantastic experience.
The Legend of Zelda: A Link to the Past / Ocarina of Time / Breath of the Wild
Super Mario Bros. / Super Mario World / Super Mario Galaxy
Kingdom Hearts 1 and 2
Resident Evil 1, 2 and 4
Final Fantasy X
Persona 3
Dragon Quest VIII: Journey of the Cursed King
Heavy Rain
Banjo Kazooie and Tooie, the entire Kirby series (yes, even the spinoffs) Luigi's Mansion, UNDERTALE and Slime Rancher! Recently got into Slime Rancher and it's the greatest game I've played in a while!
Pikmin 1 2 3
Mother 1 2 3
Miitopia
Fire emblem 3ds
all of core Pokemon
ANIMAL CROSSING
harmonknight ( tho that final boss geeeeze )
Pmd ( well mostly all )
MARIO 3D PLATFORMERS
zelllllda
Ff7 and possibly X tho I've never played it
Tomodatchi life ( you know it )
Heroes of the Storm ( only and favorite mobs I've played so I MUST be biased towardd it )
Toontown Rewritten Best MMO right?
Paper Mario 1 2 3
MandL PiT, paper jam dream team the whole shabang
Dkc reboot and snes 2
Smash Bros
Kidick ( edit. What was I typing! How could it have gotten auto corrected like that! )
I don't want to make this last the rast of this page so I'll stop