Super Mario (franchise)/Heartwarming

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.
- The Stinger always makes me tear up.

Congratulations Mario! You accomplished the 30 years of work. But your adventure isn't over yet. So, let's go to the next stage now!

- The 25th Anniversary video for the original Super Mario Bros. also has a great ending, stating that "Mario Saves Peach Forever".
The ending of the original Mario vs. Donkey Kong for GBA after defeating the True Final Boss: Donkey Kong breaks down crying, having failed to keep the Mini-Mario toys he had stolen from the toy factory. Mario, seeing this, takes pity on the big ape, and comforts him, even giving him a Mini-Mario toy to call his own.
The scene where all the characters in Paper Mario: The Thousand-Year Door are sending you hope and support to defeat the Shadow Queen is definitely heartwarming in itself. see it here