Bowser of all characters gets one in Super Mario Sunshine when Bowser Junior reveals that he knew the whole time that Peach wasn't really his mother, but he still wants to follow in Bowser's footsteps. It was just sweet to see some father/son bonding, even if it is between two evil turtle-dragons.
The end of Luigi's Mansion. Mario is turned back to normal after his painting is rescued by Luigi. He humorously crashes through the machine that turned him back to normal's opening. Luigi cries from both the relief that Mario is finally safe, and from laughing so hard at the vent stuck around Mario's head.
The first time you rescue Princess Peach in Super Mario Bros.
Though it's not a part of the games, this tribute made for Mario's 30th Anniversary is likely the most beautiful celebration of Mario's history out there. According to the description, it was a joint effort between fans and the creators of the Mario games, making it even more heartwarming.
And beforehand, there's the first part of the opening scene. Even though it marks where things start going wrong, seeing Donkey Kong falling in love with the Mini-Mario Toys he sees on the TV is very uplifting. It makes sense when you consider that the newer Donkey Kong, the offspring of the original (known as Cranky Kong), is shown to be one of Mario's friends!
It is very minor, but in one of the character pictures for Mario Golf: Toadstool Tour shows Wario and Waluigipracticing golf◊. Now, as we have seen in the trailer, Waluigi seems to be a very poor golfer (probably because it's his first time), and the picture shows him ready to strike the ball. But, you actually see Wario, being far more experienced, teaching Waluigi to golf properly by correcting his posture by using the chin-up method. It's very rare to see Wario caring for Waluigi and showing he isn't all about greed and power, even despite their constant bickering.
In Super Mario RPG, you can read the wishes of people. Two are particularly sweet.
Please let Mallow find his way home.
I wanna be a great plumber like my brother Mario.
You know what's sweeter? They both came true.
A brief moment in the ending of Mario Super Sluggers shows Daisy escorting Bowser and Bowser Jr. on her cruiser for the party. Granted, they received very little food at the party, but at least they were forgiven for trying to take over the Baseball Kingdom.
In Mario & Luigi: Bowser's Inside Story, when Princess Lipid asks what Mario has dropped, a treasure of everlasting wonder or the shabby, moustachioed man, she automatically assumes it is the treasure chest. Mario, however, says, that Luigi is his brother and is therefore far better than any treasure.
Wario working along with Mario, Luigi, & Yoshi to save the princess in Super Mario 64 DS. Of his own volition.
Talking to most of the Toads as Luigi usually solidifies his No Respect Guy role with them barely acknowledging or recognising him. One Toad however, idolises Luigi deeply, and will only entrust a star with the player if they are as him.
In the 64 version of Mario Tennis, Wario and Waluigi decide to crash the heroes' tournament. As things start to heat up, Bowser and Boo make a sinister entrance in the Doomship...and gesture for a friendly match from Mario. Why not?
The movie has the scene where Luigi and Daisy say goodbye.
Mario: (to Luigi) She's tryin' to tell ya she can't leave until she knows where she belongs. And if you loved her, you'd understand that.
When Daisy is reunited with Danielle in the Mushroom Kingdom. Ever since her abduction, she'd be scared and alone in a very creepy world. Danielle, who only met her once before, hugs her and introduces her to the other kidnapped women, who clearly had gotten to know one another and banded together during their imprisonment.
On Sunday, September 13th, 2015, the world celebrated the 30th anniversary of the Super Mario Bros. franchise. While that in itself is all varying kinds of heartwarming, a special mention goes to the prolific official Sonic the Hedghehog Twitter account for this tweet that speaks for itself. It shows not only that corporate rivals can come together in times of celebration, and can acknowledge and appreciate the other's history and success, but it is also symbolic of how Mario and Sonic themselves have gone from not being mutual enemies to friendly rivals, appearing in each other's games, as well as Sonic having games exclusive to Nintendo consoles since 2001.