The scene where Nyx turns Fluttershy into a tree (at Pinkie Pie's behest, and with Fluttershy's consent).
Fluttershy (on being asked what it was like to be a tree): It was…nice.
When the Cutie Mark Crusaders sneak into Nightmare Nyx's castle and find the purple eye-shadow she uses as 'Nightmare Moon': "Wow, that’s a lot of makeup. Didn't know you were into-" "I-I’m not! It’s just that everypony here keeps expecting me to-" Who ever expected to see Nightmare Moon, of all ponies, flustered?
The last chapter of the story, in the second to last scene, Celestia has to go and deal with a certain pony's DRAMA! moment, and tells Luna to save her only a single, small piece of cake, claiming that she still has her figure to take care of. Luna asks a servant to save an entire one to be left in her room. TrollLuna anyone?
When Apple Bloom explains to Nyx about a Pinkie Pie promise, and, of course…
Pinkie Pie: FOREVEEER!
Twist: If It's okay with you, Apple Bloom, I think I'll just use a normal promise.
When Nyx and her classmates are putting a play about the Mane 6 defeating Nightmare Moon, Applejack and Pinkie Pie comment on how accurate their dialogue is.
Pinkie Pie: I said that... I said that! This is so cool! They got everything just right.
Applejack: That’s mostly because of you, Sugarcube, since you somehow remembered everythin’ we exactly said.
Pinkie Pie: Oh, that was easy. I just read the transcript.
That's right, the transcript to 'Friendship is Magic, Part 2.' Try not to hurt yourself when you fall out of your chair.
After everything is all said and done, Nyx is back to normal. Her one question to Twilight?
Nyx: "I know Luna already gave me her judgment, and I'm glad to be a filly again, but…well…I did do a lot of really bad things. So, I was wondering, and if you say yes I promise I won’t get mad, but…am I grounded?"