Shining realizing he was wrong about Nyx and the two of them making peace and amends. As the narration puts it:
When repentance is offered, forgiveness should be given.
Bright Eyes waiting patiently in line with the other petitioners to the throne, just so he can ask if Nyx can come out and play and if he can use the bathroom. He gets a laugh from the room, but not a mean-spirited one, and Cadence is quick to accommodate him on both counts.
The reason Spike managed to Hulk Out and keep control? The bastards were trying to slaughter his "hoard", aka every pony he knew.
Spike: You know how Celestia says "My little ponies?" Well, it seems stupid but... I feel the same.
When Spike threatens Garble with bloody murder if he ever tries anything again against his "hoard":
Spike: Shining Armor? He's my uncle. Princess Cadence? My aunt. Twilight Sparkle? My mother.
Nightmare Night and Nyx:
Fluttershy thinks Twilight is a wonderful mother to Nyx.
Celestia and Nyx making peace and amends.
The original Cutie Mark Crusaders finally get their cutie marks, all on the same night.
Nyx and the crusaders accepting Flitter the changeling filly as a friend.
Flitter: I'm a monster.
Nyx: Hi, maybe we haven't met. I'm Nightmare Moon. Maybe my big brother the dragon can introduce us?
Ink Spot's Big Entrance (see main page) was motivated completely by the fear of losing Twilight. And then he proposes. With a ring topped by a diamond he stole from a Diamond Dog, which makes the whole scene awesome on top of heartwarming.
While the drama of the moment makes it a Crowning Moment of Awesome, seeing Celestia going Mama Bear over Twilight was endearing as well.
"DID YOU IMAGINE FOR A SECOND THAT I WOULD REFRAIN FROM BRINGING MY FULL POWER AND WRATH TO BEAR AGAINST ANYONE WHO TRIED SUCH A THING WITH MY MOST BELOVED STUDENT?"
Rarity's developed explanation of her relation with Spike to Zheng He and Pelé.
Rarity: When he was lying there in that hospital bed... he told me that the reason he had fought so hard was... of all the things he had, that I was his greatest treasure. Me. Not Twilight, not Celestia. Me. What else could I do but finally fall in love with him?
Nyx, Killdeer, and Doubloon meeting for the first time is pretty sweet.
Doubloon taking the blame for the drain incident.
The Royal Kids — Killdeer-Adder, Doubloon, Gossamer, Songhili the Selkie pup, two blue-flame Phoenix chicks, and Po, a servant of Zheng-He (whom was doted upon by Zheng-He) — and the Cutie Mark Crusaders having a movieevent in Twilight's quarters. Then, the Royal Kids have a sleepover.
Prince Blueblood is punished for his family shenanigans (which he helped to stop) by being assigned to trade routes. But then he reveals that this is what he wanted all along: "A tall, tall ship, and a star to guide her by."
Po's talk with his master Zheng He, who reveals he loves him like a son.
Time Turner proposing to Ditzy, and buying a new house for them to live in.
Why does Twilight want to abdicate? Spending the equivalent of five years working on the Cosmic Synchronizer made her realize how much she was missing her friends and family, and she was done allowing anyone else to dictate the course of her life so she couldn't see them.
By that same token, Celestia praising Twilight for finally having the courage to tell her NO and reject a future she doesn't want.
Ink Spot ascending at his and Twilight's wedding.
Silver Spoon has an emotional breakdown while reading a scary story for the class with the lights out, and Willow realizes she's terrified of the dark. He and the rest of the class light up the room to comfort her, using everything from horn lights to a birthday candle, and he gets his cutie mark.
Flitter recalls the first time she met Pound and Pumpkin Cake. Pumpkin took one look at her, ran off crying - and then came back with a first aid kit to put Band-Aids over the holes in Flitter's legs. Flitter nearly melted on the spot from all the cuteness.
When Snips and Snails find out the reason Willow scared them so badly was because he thought they wanted to hurt him, they're shocked that anyone would be so cruel. They may be idiots but they're nice idiots.
Snails' crush on Doubloon is also adorable, especially since she reciprocates.