* The [[InterspeciesRomance Koopa Troopa/Boo couple]] in Bowser Castle. Doesn't seem like much on the surface, but if you think about it, [[ThePowerOfLove their love]] was strong enough to persist even after they were {{brainwashed}} into being Fawful fans.
* The ending, where [[spoiler:Bowser, while nursing his wounds after being beaten by the Mario Bros. gets a gift from his enemies: [[http://www.mariowiki.com/images/e/ea/EndCake_MLRPG3.png A cake]] with little figures of Mario, Luigi and Peach and Bowser's face right in the middle.]]
** Even more so in that he's always wanted Peach to make one for him ever since ''VideoGame/SuperMario64'' back in 1996.
** Starlow being the one to deliver it is also heartwarming, considering the OddFriendship of sorts she and Bowser had developed throughout the game.
** In Bowser's "memory banks", after failing to repel the Bros., the synapse running the place takes the shape of a pixelated Peach for communication purposes. The synapse says the shape is based on "the host's most carefully preserved memory".
*** Likewise, using copies of Mario and Luigi as his defense against intrusion into Memory Banks. Shows some respect that rather than following his ego, and having a fake Bowser to fight there, or even an army of his minions, he has deep seated enough respect for the Bros' strength that his mind chose THEM as his defense.
* [[http://www.youtube.com/watch?v=G-wNoaqvuAc This theme]] (known as "Friend theme"). It's played whenever Bowser's friends are around (Broque Monsieur, Private Goomp, Sergeant Guy, Corporal Paraplonk). Even though he may be a villain, he does have friends who help and support him, which makes it all the more heartwarming.
* Bowser and his minions. Specifically the ones Bowser rescues from the cages. There was this odd sense of... almost ''family'' going on between them, with Bowser being the classic gruff-but-devoted TeamDad. After viewing Bowser as a {{Jerkass}} tyrant for years and years of games, it's both odd and touching to see that some of his minions genuinely like him and want to serve him.
* Luigi's [[OcularGushers reunion with Mario]] early on in the game is a perfect blend of this and CrowningMomentOfFunny, and just all-around ''very'' easy to smile at.