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 the first level, there are two sleeping Waddle Dees backed up against each other. A heart made of beads is above their heads.
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 apoligize 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.