The level with Eely-Mouth. After you clean his teeth, he spits out his golden tooth (actually a Shine Sprite) and leaves behind a heart made of coins. Eely-Mouth is saying thank you. Awwww.
When FLUDD seemingly passes away, Mario not only looks depressed but he also seems to be wiping away tears from his eyes. F.L.U.D.D may have simply been a robot with artificial intelligence to most people but to Mario he was a true friend.
The scene with Bowser and Bowser Jr. at the end, oddly enough. You can actually see a tear forming in Bowser's eye when he's trying to break it to Junior that Peach isn't his mother... only for his son to reveal that he knew the whole time, or figured out somewhere along the line, that Peach wasn't really his mother And then we get this line.
It was just sweet to see some father/son bonding, even if it is between two evil turtle-dragons.
Even though it wasn't very successful, Peach trying to vouch for Mario's innocence in the game's opening shows how much she cares about him.
The Noki in general are really nice to Mario, which is odd given he's currently considered criminal until they drop a few hints about knowing he's innocent. The Noki are a small minority most places on the island but they still go out of their way to be nice to someone who is being mistreated by the Piantas and seem to be the first locals to act in his defense or go out of their way to be helpful.