* 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.
** Particular mention should go to the part after he rescues the Goombas and gets Goomba Storm, and a Fawfulcopter shows up and Fawful taunts him by showing him various minions in trouble. You can actually ''see'' his expression changing from neutral to ''pissed off'' as he sees his minions being captured.
* 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.