Zelda going to sleep and Granny Impa's passing in Skyward Sword.

Emmeryn's death, Chrom learning 'Marth' is his daughter Lucina, Lucina wanting to kill Robin, and the Robin's sacrifice ending of Fire Emblem Awakening.

Rosalina's story in Mario Galaxy.

The 'you've unlocked every character' screen in each Smash Bros.

These two got me good too. 

The ending of Mario Galaxy where everything is being sucked into the black hole and the lumas dive into it to restaret the universe always brought a tear to my eye as well.

Probably Xenoblade 3 has the most emotional moments.

Reminding myself how great of a game Xenoblade 3 was and its story.

I thought it was neat when they broke the fourth wall in Yoshi's Island for SNES. Oh, and also on the very last special level of SMW.

Yeah Chapter 5 in XBC3 messed me up, easily one of the most gut-wrenching moments of any game I've played, Nintendo or not.

Elite Beat Agents has this Christmas themed comic about a girl waiting for her father to come home, played to a version av "Your the inspiration". That first playthrough of it had me tearing up, probably the only time ever from a video game, and it is a bloody music game?!

A few moments from Zelda Skyward Sword stuck out as emotional for me. That time when Impa turns around and tell Link that he is to late, that one hit my gut. Also pretty much all character development moment involving Groose, bully turns buddy is a story trope I often like.

Meeting trainer Red on top of the mountain in Silver/Gold/Crystal. Pure gaming magic and probably a core gaming memory for anyone who grew up playng the first few generations of Pokémon. It does not strike as sad the same way other emotional moments does, but it certainly make the game world feel real in a sense that is very emotional.

Chapter 7
-The Telescope-

Golden Sun: The Lost Age. 

Welp, emotional doesn't mean just sad really but it's difficult to not rank the saddest moments or disturbing ones in Nintendo games because they do stuck out incredibly in contrast to their usual affairs.

Here's my non-exhaustive list :

- Mother 3 ending sequence has a whole.

- Famicom Detective Club Emio last chapter and the epilogue has easily the most disturbing and mature content of any game they published before.

- Xenoblade Chronicles series is basically chock full of incredibly diversed emotional moments notably, the ending of Torna, XC3 Chapter 5 and many others, any time Tomorrow with You plays in XC2.

- Super Mario games ending sequence are usually some of the happiest moments you can be while playing these games (Except Galaxy 1 lol)

- Kirby games have the hypest final boss attack moments you could want. 

On the broader spectrums of emotion beyond poignancy/sadness, the climax of New Donk City in Mario Odyssey was one of the most joyful experiences in my entire 32 years of being a gamer, just magical.

Same goes for the climax of the game itself, I had a big dumb grin on my face the whole time.