While also a Tear Jerker, this flash animation ends on a touching note. Trixie, having finally snapped under the pressure of hitting rock bottom and losing everything, runs outside in tears, trips and knocks herself out. A pony implied to be Luna finds her and tucks her into bed, leaving a large sum of money for her along with a note reading "You are not alone" signed "Your #1 Fan". Even more touching when you think why Luna would do something like that, given her background, she knows exactly how Trixie feels to feel like she's all alone.
The last quote on this selection of Derpy voice clips. Dinky asks Derpy if she still can't eat muffins, Derpy tells her of course she can. Dinky is overjoyed to hear her mother back to normal, presumably after her Discording.
Philsterman does it again! In particular, what he says toward the end:
Philsterman: Nopony deserves to be sad. So think of the happiest thing you can. And smile!
This will make you weep from all the heartwarming.
This music video with Zecora singing "Dig a Little Deeper". The segment directed at Spike fits particularly well in context of the show. The last verse directed at Twilight is less applicable, but the clips chosen makes it heartwarming nevertheless.
The Fluttershy edition of My Little Pony in Thinking with Portals, which features her trying to use the Portal Gun in hopes of staying over with one of her friends during a stormy night, with Rarity, Applejack, and Rainbow Dash showing up at Fluttershy's home (via Rarity's custom Portal Gun) near the end after Fluttershy discovers that they're not at home.
MandoPony's song for Zecora, Home, is a heartwarming tale of Zecora moving from one place to another in search of a place she could call home, and eventually finding it with a little help from "a little one with a pretty bow in her hair". Made doubly heartwarming by the fact that the song is also about Mando himself, from his moving around a lot to befriending Michelle Creber, the VA of said little one.
This song, titled "Great to be Different" becomes all the more sweet when you learn about its backstory—the creator, while selling paintings at Bronycon, left his booth for a while to look at the others and came back to find a plain old letter on his table. What did that letter say? It simply said, "It's great to be different! Love, Derpy." That letter is the most prized possession he took home from Bronycon, and the message it had stuck with him ever since, which led up to this song. And as the song proves, it IS great to be different.
How do you turn an originally villainous and chilly song into an heartwarming one? By having Princess Luna sing it to orphanage foals, bringing them with her and flying away with them into the night and a hopeful future.
Snowdrop is an amazing video about a blind filly and her gift to the Princesses. It's absolutely adorable and heartwarming.
In the YouTube video The Joker Meets My Little Pony, it's touching that Batman beats the crap out of The Joker after he threw Applebloom into a garbage can and made her cry. Especially at the end where Batman and Applebloom say their farewells, with Applebloom stating that even though they just met, she'll miss him. Batman then smiles at her and pets her.
The ponified video for Hijo de la Luna despite being a generally Tear Jerker song has a rather heartwarming ending. Luna adopts the newborn colt as her son and uses the moon itself to cradle him to sleep.
Derpy's Toy starts out as a bit of a tearjerker, but by the end becomes one massive ball of heartwarming.
Leaving You is a short and simple animation about Angel Bunny preparing to leave Ponyville. Fluttershy finds a letter written by him and rushes to find him, even though the train that Angel had boarded had left the station. She eventually finds him, making for a very heartwarming ending in what would otherwise be a massive Tearjerker.