It's the last thing you'd expect from a fic like this, but this alternate ending definitely qualifies. In short: Pinkie Pie wakes up, revealing that the entire story was a bad dream. A few minutes later, she appears at Rainbow Dash's front door, bawling her eyes out. When Dash asks her what's wrong, she gives her a massive hug and says, "I just needed to make sure you were all still there." Awwwww.
The Light in the Darkness was originally written as an Alternate Ending to Cupcakes (and can still qualify due to the vagueness of the dream) and has gained appeal as one of the most heartwarming fics in the fandom. Yeah, that's right, the fanfic which has obtained The Scottish Trope level infamy among the fandom has spawned what's considered one of the most heartwarming ones.
This comic has a few. A copy of the fanfic is randomly appearing in front of the Mane Cast. The heartwarming comes from the fact the rest of the mane cast never doubt Pinkie's character for a second. A more major one comes from when Rainbow Dash reads it. Pinkie is crushed when she sees she's reading it and desperately pleads with her not to believe it. Rainbow bursts out laughing, considering the fic the funniest thing ever. Why? Because she knows the real Pinkie would never hurt her and ends up being the one to cheer up Pinkie.
The ending to Cupcakes: Consequences. certainly qualifies. Pinkie's behavior was caused by a Parasprite in her head. After realizing what she's done, she requests Celestia turn her to stone, and is granted this. As time goes on, ponies begin to notice something strange about the statue — namely, that no foal ever gets hurt in the park where it stands.