The Waddle Dees in Kirby's Epic Yarn seem like they would rather pal around with each other than get in the way. Try not to stop and smile at them playing catch or even just falling asleep where they stand.
In fact, playing any Kirby game, especially the old ones, qualify as a heartwarming moment because of the sheer amount of nostalgia fuel within them.
The part of Super Star where Meta Knight orders his followers to evacuate the Halberd. When they insist on staying to fight Kirby, he acts like he doesn't care what happens to them, and it sounds like he's trying to get them mad enough to leave so they won't get hurt. Then he apologizes under his breath, either for snapping at them, getting them in danger in the first place, or said faking of indifference towards their fate.
A minor one, but after the credits of Squeak Squad, we find out that the Squeaks sent Kirby's cake back as an apology for causing so much trouble. It's such a nice thing to do, especially after Kirby endlessly beat them all up just for that cake slice.
A more minor one, but in Kirby's Dream Collection, Magolor states that after the events of Return to Dreamland, he wanted to apologize to Kirby by building him a theme park. He actually means this, and that the only action that even closely resembles maliciousness is attacking you when you race.
The credits for that section of the game is another one with the music alone, if you're a longtime fan of the series.
Heart Warming In Hindsight: Air Ride was the last game that Masahiro Sakurai was personally involved in before he left Nintendo to found his own company. At the time, there were rumors floating around that he considered Air Ride to be an Old Shame due to the amount of Executive Meddling involved during development. However, every project Sakurai has worked on since then has had at least one thing in common with Air Ride:
Brawl and Kid Icarus: Uprising borrowed the way that certain features were unlocked via a large grid that slowly revealed more objectives the more you unlocked, along with a tool to bypass certain objectives that the player found too challenging.
The concept of the Dragoon and the Hydra: a potentially game-breaking ability that's divided into three parts that players have to collect or fight over before it can be used. Not only did the Dragoon appear as an item in Brawl, but this is also how Day Break works in KIU's multiplayer mode.
And finally, the recently-announced Smash Run mode from the 3DS version of Smash 4 was explicitly stated during a Nintendo Direct to have been inspired by Air Ride's City Trial mode.
Looks like Sakurai doesn't hate Air Ride after all!