- The entire backstory. Yes, the whole darn thing.
- When Luvbi told her parents she loved them before turning into her true form, even after being hurt about the truth. Awh.
- And then 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...
- Bowser, Peach, and Luigi's Big Damn Heroes — which finally triggers the Pure Hearts to negate Bleck's Chaos Heart-based invincibility. Likewise, unlike most villains in Not So Invincible After All situations, Bleck is genuinely proud of them for being able to pull it off (though this one does overlap with Tear Jerker; he's after Suicide by Cop).
- 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 where they reaffirm their love for each other, all leading up to the last scene mentioned right above.
- The end screen is the piece de resistance. Blumiere and Timpani, returned to their true selves and together at last, standing on a Ghibli Hill as their flashback theme plays and the wind blows. They embrace, then walk over the hill together out of sight.
- In World 5, Mario and co. find a crag named Gabbro hiding in the Floro Caverns with a Pixl named Dottie. Turns out Dottie was helping him hide because she sensed his fear and kept him company until Mario found her. Even after her and Gabbro part ways, he expresses his gratitude towards her and she (in a rather eloquent manner) laments how his absence affects her.
- 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.
- Visiting Squirps in the Whoa Zone has him recounting how sad he was that he had to leave his mother, but that he put on a brave face because of how big a responsibility he had. He goes on to promise her that he will restore their kingdom someday - a pretty big dream for what seems to be a very young child. Likewise, tattling Squirpina's statue has Tippi state that she is always watching over her son. Awww...
Heartwarming / Super Paper Mario