Fluttershy comforting Twilight after she finds her way back to the Loyalists' base.
That being said, Twilight's reunions with all of her friends qualify... except Rainbow Dash, who can't bring herself to get over what Nihilus did to her. Which makes their eventual reconciliation all the sweeter.
Similarly, Twilight's reunion with her parents, who thought she was dead.
The Reveal that Spike is still alive after Twilight had been told he was dead.
After Titan is killed, Twilight and the others convince Terra to use her knowledge of Harmony's power to help Twilight save Rarity's life, thus beginning Terra's own path to redemption. Afterwards, the seven of them just sit atop the Citadel and watch the sunrise.
Twilight, who is utterly convinced she deserves none of the respect her soldiers give her, makes a Rousing Speech. Dash's reaction?
Rainbow Dash: *quietly* And you think you don't deserve their loyalty.
Discord saving them from Titan and giving Twilight a chocolate fudge sundae with a note "You've earned it." Sure, he's not that much better than Titan to begin with but considering the crap Twilight went through, it was a nice gesture.
Rarity embodying the element of generosity and giving up not only her life, but her only possession in the world for Twilight. The fact that she lives though it is even better.
She'd kept the weapon hidden. She'd kept it secret. She'd kept it to feel safe. Above all other things, she'd kept it. Now it was the only thing she owned. The only thing that generosity had left to give.
Twilight finally forgiving Celestia, and her final words to her friends before she absorbs Harmony's divinity.
I love you. All of you. And I love Celestia, too. Make sure to tell her.
Applejack and Rarity's reunions with their sisters in the epilogue.