I think I go with Tokyo Mirage Sessions. Yeah, Atlus made it, but with Nintendo involvement.

Donkey Kong Country trilogy. I know it's made by Rare but it's a Nintendo IP.

Mario Galaxy 1+2.

Why it deserves this pick?
Its the best 3D mario game(s) made, platforming with gravity, and 360 degree, usage of platforms works wonderfull.
The small puzzles and fights, are fine too, and again the platforms often being sphere shaped, allows for intresting usage of such.

Then theres the view while playing it... played on a pc, via emulator upscaled its still the best looking mario too date.
I love the style of its graphics.

Greatest game is a very broad range especially as Nintendo goes because you can do a top 20 with them, their greatest game imo will always be SMB because it lead to what we have now it's impact and legacy can only be matched by Pong, favourite game from them is BOTW currently.

Either Super Mario Bros 3 or Super Mario Galaxy.

If I had to pick one, it'd be Galaxy. Fantastic level design, fantastic gameplay, fantastic music, and a 60fps framerate. Incredibly fun to play, which is all that matters, right?

I love the game, but the lazy level design and the glorification of the J-pop industry (which is known to be very brutal and exploitative) seriously stop me from even considering a top 10 spot for the game from me.

Super Metroid is probably my top seed. I had been gaming for a decade when it came out. But, it was the first game that really sucked me in. All day at school I would count the hours until I could get home and play. And, as others have said, its just an all around great game.

If we take sentimentality out of it, BotW is probably the more objective winner. I will note that the DLC for BotW was disapointing, and probably actually detracts from my love for the game. I'd have preferred not to come back to it for mediocre content that really just tarnished my memories of an otherwise excellent game.

The movie: Run Lola Run was the inspiration apparently.
https://gamnesia.nintendoenthusiast.com/aonuma-reveals-the-inspiration-for-majoras-mask/

I would have to pick 2, but of course they are already mentioned. OoT. It's not a fair comparison to other Zelda's,because this was the first Zelda I played, so it felt completely original, in contrary of most of the other Zelda's I played. But the world felt complete and believable, and the time travel really made me feel like the mythical warrior. It really gives the game an extra layer. And normally I don't like levels/worlds with changing water levels, so in my memory, I didn't like the water temple. But when I replayed the game on an emulator, I thought, this temple is so good, it's impossible I didn't like it in the past, so my memory has to be wrong. And the game doesn't have weak temples or bosses. I also really liked the final castle and the fights with Ganondorf in all his forms. For me, this game had everything. You can really notice that Nintendo has worked on this with almost his entire team, because (for that time) the game had no points where you could say. That should have been better.

The second game is Mario Galaxy 1. Everything about the levels was perfect and what it did really well compared to Mario64, was the live music and variety. No grinding like get 8 red coins and 100 coins in every world. So if you had to get 100 coins, it was fun and it was a challenge. Replaying the game with Luigi felt really fun as well and just different enough from Mario, that it didn't feel like replaying the same game. The only thing that could have made the game 'better' was adding the yoshi levels from mario galaxy 2. But overall, the game is so extremely fun to play, it's already a big 10. Really hope they bring it to switch, one way or another.

That is also the best game ever created period;

The Legend of Zelda: Ocarina of Time.

Metacritic agrees with me.

Nintendo inhouse games I’d rank a top 10 like this, lots of Mario and Zelda, but I guess it just is what it is;
1. Zelda Ocarina of Time
2. Super Mario 64
3. Yoshi’s Island
4. Zelda Link’s Awakening
5. Mario Kart 64
6. Zelda Breath of the Wild
7. Super Mario Bros. 3
8. Zelda Twilight Princess
9. Super Mario Galaxy
10. Metroid Fusion