When you put a Scarf on one snowman and a bucket on another, they'll grant you entry to the Crystal Palace and reward you with 4 Mushrooms and an Ultra Shroom the next time you spend the night at the Shiver City inn.
The Thousand-Year Door
When you defeat Hooktail, she coughs up Koops' dad Koopley, who has been living inside the dragon's stomach for 10 years, making a heartwarming reunion ensue.
Another one happens when you free the other 90 Punies. Punio reunites with his little sister Petuni, who gives him a Dried Shroom. It was supposed to be a Mushroom, but she and the other Punies were imprisoned for so long. He eats it anyway, even though his disgust at the flavor is practically visible.
In a finely executed Call Back, the two siblings show up at the very end to wish you and Peach farewell... and they have fresh Mushrooms this time.
Yet again, another moment of heartwarming occurs after you defeat Macho Grubba, when it is revealed that X is Jolene, who has sent Mario messages on his Mailbox SP because her brother, Prince Mush, has vanished and Grubba was responsible. Prince Mush came back and reunited with his sister.
How can you forget Admiral Bobbery? A letter written by his dead wife finally convinces him to return to the seas after a long, tear-invoking scene.
Vivian deciding to stay on your side in Chapter 4's climax.
Especially when the game decides to inform you: Vivian has REALLY joined your party now!
It's been said before (though I can't remember where exactly), but before fighting the final boss, there's a sequence where you see characters sending encouraging messages/thoughts/whatever to Mario before facing the aforementioned boss. One that appears several times over, 'written' in green is "You go bro"— as insignificant as it is, it always makes me smile.
The whole ending of the game, staring with the initial good-byes of all the characters at the harbor, showing how all Mario's partners have grown over their adventure. Then, Goombella's e-mail tells Mario how everyone is doing, how everyone's lives got better because of Mario.
Prior to that, for similar reasons, the most uplifting part of the Hope Spot scene during the final fight might not even be hearing the good wishes of all the friends and admirers Mario has made over the region - a large number of the speech bubbles that start filling the screen in the cut back to the palace are cheers for his by then definitely player-beloved partners.
No mention of Bub's trouble? After beating the game, a request at the trouble center opens up, which involves you helping Bub to make up with his mom after a fight. The letter Bub writes to her as well as his mother's reaction to it is truly touching.
It's a small one, but the fourth cursed chest thanking Mario for letting him give a huge speech was touching.
This line from Flavio towards the end of Chapter 5 just before he asks Mario to take him to the Pirate Spirit Cortez (the chapter boss) to bargain for use of his ship to defend the crew from the X-naut vessel attacking the beach:
Flavio: Hey! I may be a coward and a cad, but I still lead you! I have a duty to protect you!
Super Paper Mario
The entire backstory. Yes, the whole darn thing.
But this one takes the cake. "A world without her is empty... a life without her is empty." AWWWW.
And the scene at the very end showing that Count Bleck and Tippi (in her original body) finally found paradise and are standing together on a hill with their theme music playing?
When Luvbi told her parents she loved them before turning into her true form, even after being hurt about the truth. Awh.
More heartwarming! The Power of Love prevailed and despite Luvbi being a pure heart, she is at her parents' side at the end of Chapter 7-4
In the intro, you could see that Mario has group pictures of his partners from both games inside his house.
The entire ending is one big heartwarming moment, but there's a subtle one right as everybody (minus Peach and Merlon) leave the stage. You see Bowser try to barrel through the crowd, the minions turning around and leaving... and Mario turns around to face Luigi, who nods and follows him off screen. Particularly touching, after that final boss...
Pretty much everything after the fight with Bleck, except for when Dimentio is on screen. We have Nastasia taking Dimentio's attack for Bleck; Tippi, Bleck, O'Chunks, and Mimi showing so much care for each other that the Pure Hearts are revived to weaken Dimentio; and Tippi and Bleck's Heroic Sacrifice, all leading up to the last scene mentioned right above.
In World 7, the scene where Luigi and Mario reunite.
Talking to Red and Green after saving the world shows in spite of their disdain for each other's choice in clothing that had driven a wedge between them, they really care about one another and want to make amends.
Likewise, talking to Old Man Watchitt shows he wishes Bestovious lived in town so that they could talk more often as even after all the trouble they've had over the years he still considers him his friend.
Paper Mario: Sticker Star
Saving the Toads.
Wiggler is so happy once Mario helps him out in Chapter 3, that's pretty heartwarming. It doesn't stop there either, Wiggler grows up into Flutter, and helps Mario get to World 6 in order to return the favor.
What does Mario do when he has all of the Royal Stickers and gets to make his wish? Restore Kersti back to life. Aww.
The credits sequence shows everyone in the game happy and smiling, even Mizzter Blizzard, who has come back to life.
Bouquet Gardens has Toad crying over a former flower patch (which was blown away by the Fan Thing). Paperizing three Fire and/or Ice Flower stickers will cause the flowers to grow back. After this, Toad proceeds to happily watering the new flowers.