- Chapter 1: The Koopa skeleton holding a farewell note in Hooktail Castle. Koops believes its his fathers skeleton, though it turns out its not. It's Kolorado's father.
- After defeating Hooktail, she spits out Koops real father and they have a heartwarming reunion.
- A rather minor one, but still sad: after Chapter 1: Mayor Kroop of Petalburg puts in a trouble at the Trouble Center requesting that someone come talk to him (exact words: "Will someone please talk to me? Please?"). Considering it's already a Running Gag that Kroop is a crazy old senior who rambles for so long that those listening to him fall asleep, the trouble, of course, is Played for Laughs, but consider the predicament of many real life seniors who wind up friendless and lonely in their old age, and the event suddenly becomes much sadder. And leads to a Heartwarming Moment when Mario takes the trouble on.
- Chapter 3: Jolene reveals that she was the mysterious X person who helped you discover Grubba's evil secret. Her motivation for this was because her little brother, Mush (aka Prince Mush, the first champion of The Glitz Pit), went into fighting to provide money for his poor family. Then Grubba made him vanish. She just wanted revenge for her brother's disappearance.
- Chapter 4: Vivian pulls a HeelFace Turn during the battle against Doopliss at the end of the chapter. She decides to help Mario because her sisters treat her like dirt and that he was one of the first people who was kind to her.
Flo: He studied so very hard, and we spent so very much.
- One of the Trouble Center missions has you acting as a runner between Eve, a woman in Twilight Town, and Podley, her former lover. He's changed a lot since then, and pretends not to know her. But just as you leave the bar, you hear him whisper, "Oh, my Eve..." When you tell Eve that he's forgotten her, she acts like she understands and gives you your reward. And then you leave, and through the door you hear one of her children ask, "Mommy, why are you crying?"
- Also found in Twilight Town, Mario can enter on of the homes to find a mother and her 3 children, all starving because their father has been turned into a pig due to the curse that plagues the town. After asking Mario for some food, the mother is interrupted by the ringing of a bell and gets turned into a pig herself. Two of the children seem quite upset about the situation, while one calmly asks Mario if pigs are a 'good eat', giving some frightening and sad implications.
- Pretty minor, but still a tear jerker nonetheless. When you use Vivian's field ability to eavesdrop on some of the Twilight Town birds, one bird states that her son is getting ready to take his SAT's. Come back later and she reveals the poor kid failed.
- Chapter 5: Perhaps the biggest one in the game is Bobberys letter from his dead wife, Scarlette. When Podley said that his friend's story was a tragic one, he wasn't kidding.
- Each partner also has their own reactions to hearing that story. Ms. Mowz's in particular goes, "Why do most romances have to end in tragedy? Why?"
- After fighting off a group of ghosts by himself, an injured, presumably dying Bobbery asks Mario to fetch him his bottle of Chuckola Cola, the one he had been saving for him and Scarlette, so that he could savor one final drink before expiring. When you get it for him, the heartbreaking music kicks in as he takes his last drink, then utters how he'll finally be with Scarlette. With his final wish fulfilled, the sea captain dies peacefully... or at least, you think he does, until you realize that he just fell asleep.
- Chapter 6: Bub, son of the wealthy Goldbob and Sylvia, doesn't really care that much he's rich and just wants an autograph from the train conductor because that's the kind of job he wants, plus the train conductor's reaction that a kid actually looks up to him as well.
- Grodus ordering TEC be disconnected, and his farewell message to Princess Peach.
- When you get the Ultra Hammer and Toadette finishes her explanation, she starts feeling sad because that's the last time she'll see Mario, and she's clearly saddened about it. What really hits it is how she runs away as if she was trying not to cry...
- Chapter 7: TEC barely manages to survive on backup power and weakly tells Mario how to escape the X-Naut fortress.
- Chapter 8: Princess Peach is possessed by the Shadow Queen and Mario is forced to fight her.
- Also, all the people you have met along your adventure start to cheer you on during the battle. They're on the edge of despair and plunged in darkness, but seeing the Crystal Star show up in their area reminds them of Mario's impact on them in his adventure, and it revitalizes their hope. It definitely reflects on the player too— you've come so far, and seeing all these characters rooting for you and showing the progress you've made, is just amazing. It definitely counts as a Moment of Awesome and a Heartwarming all at once.
- All of the party members saying their farewells to Mario. It really hits you how much they've grown through the course of the adventure, and how much this group of Ragtag Bunch of Misfits has become a sort of family.
Tear Jerker / Paper Mario: The Thousand-Year Door