Chapter 4, Nyx keeps making silly and dry comments while Shining Armor is trying to drink his coffee. The orange juice was even worse.
In Chapter 4, Nyx makes a mess on Shining Armor's uniform and tries to use the washing machine herself. A few minutes later, Shining Armor is talking with his Lieutenant when they hear Nyx screaming "FIRE! FIIIIIRE!" As they soon discover, the washing machine was overloaded with detergent and created a big foamy mess. After it's been cleared up:
Shining Armor: Nyx, why the heck did you yell 'FIRE?' Nyx: Well, nopony would've come if I'd yelled 'LAUNDRY!'
And then they start smelling smoke from the kitchen, where Nyx left the soup on. "AGH! FIRE!! FOR REAL THIS TIME!!"
Chapter 12: Evil Linda! Evil Mistress of Eviliality!
Chapter 14 gives Spike two good moments. The first when, after Twilight's played a game of Break the Haughty on a Know-Nothing Know-It-All scholar, offers him ointment for the burn. Then, upon learning one of those assisting in the research has developed a means to easily reshelve an entire library with the push of a button grabs him in a hug and declares "Don't take this the wrong way but— I'm yours."
The same chapter introduces four unicorns who are thinly-veiled anthropomorphisations of Google, Firefox, Wikipedia and Defrag. The resulting puns are hilarious, especially Spike's argument with Wicker Speedy over using the term "scroll down" when the scroll in question is being rolled up.
Celestia reminisces with Luna about the good old days when she protected the people, slew monsters and, well, actually had something to do. Now that Twilight's on her own, she's bereft or anything entertaining to do, and wishes for some to drop out of the sky. And then some hapless dragons get teleported in... and find a very creepy shadow looming over them...
Celestia: Oh TWILIGHT! You did remember my birthday!
Chapter 33, the last chapter, uses the very last few paragraphs of the story to bring in a Brick Joke to a tremendous and hilarious landing. Essentially, Diamond Tiara and Silver Spoon despise Nyx. They also have a huge crush on Shining Armor, Nyx's uncle. They don't know he is her uncle. This leads to the following scene as they await Shining Armor's appearance at Ponyvile train station:
Diamond Tiara: Oh eww, you're back. What are YOU laughing at, Nightmare Ninny?
Nyx: What are you guys doing? Don't you know Prince Shining is married?
Diamond Tiara: Go away, weirdo, we don't want Prince Shining to see us standing around a loser like you!
Nyx: You dimbulbs, dont you know...
Diamond Tiara: (noticing Nyx is on the verge of bursting into laughter) What is wrong with you?
Nyx: Nothing. (''Shining Armor approaches the group. Diamond Tiara and Silver Spoon start fangirling... but then their faces fall when Shining gives Nyx an affectionate noogy)
Shining Armor: Hey Nixie stix. (''points at Diamond and Silver) Friends of yours?
Nyx: Not really.
Shining Armor: Hi girls. I believe you met my niece here?
Diamond Tiara and Silver Spoon: NIECE???!!! AAAAAAUUUUUGHHGHHGHG!!!
Nightmare Night and Nyx:
During a Cutie Mark Crusader sleepover, Twist notices a cloud from which Lightning Blitz and Sundiver, two pegasi members of the Royal Guard, are keeping an eye on Nyx to protect her from harm. Assuming that they're "pervertth", Twist warns the others, and the Crusaders soon end up driving them away with a coordinated barrage of slingshot fire and high-velocity produce.
Sundiver: Blitz? Lightning Blitz: What? Sundiver: Something just occurred to me. Something we really oughta have remembered. Lightning Blitz: Yeah? What? Sundiver: That cute little innocent alicorn filly? The one we're supposed to protect? Lightning Blitz: Yeah? Sundiver: —Once conquered all of Equestria— all by herself— in less than a week. Lightning Blitz: So you're saying we underestimated her? Sundiver: Just a tad…
From the same scene: "CUTIE MARK CRUSADER ANTI-AIRCRAFT ARTILLERY, YAY!"
In Chapter 5, Twilight shows Nyx her old hourglass, which, because she got tired of turning it over while studying, she enchanted it so that the sand perpetually transports back to the top by itself. Nyx points out the obvious problem, and Twilight admits that not all of her ideas were brilliant.
In Chapter 6, the Mane Six are preparing for Nightmare Night and Twilight has cast her Butterfly Wing spell on herself, intending to use it on the others later. When Ink Spot arrives to pick up Twilight, Fluttershy answers the door to greet him, then closes it and lets out "the loudest, most un-Fluttershylike shriek of laughter anypony there had ever heard". Finally she manages to composes herself and lets him in, revealing that he's wearing an explorer outfit with a butterfly net on his back and a field guide to butterflies on his hip. After a moment's silence, he says the only thing he can: "Heavens, I think I'm going to need a bigger net."
The scene where Celestia and Nyx completely reconciliate is truly moving, but ends on a CMOF. At the end of the scene, Celestia explains to Nyx that because of the ritual, she has a biological link to Luna and Twilight, and thus, Twilight is actually her biological mother. Nyx is overjoyed, then hesitates, and...
Nyx: Hokey smokes. Does this mean that Princess Luna is my Dad?
Twilight one-ups her daughter later on by waiting until Celestia is about to take a drink before (falsely) claiming to be pregnant. The resulting Spit Take disintegrated the glass she was drinking from, much to the amusement of Twilight, Ink Spot, Cadance, and Nyx.
The villain lists these Noodle Implements to fix his spell. ( At least one Changeling filly disguised as Nyx stole one of the necessary crystals.)
Sundae Sprinkles: "Get me three of the lesser amethyst crystals, a tourmaline, some duct tape and a banana!"//
Which is given a Call Back later, by, of all people, Spell Nexus:
Spell Nexus: "They must have used a substitute! I wonder where they found duct tape and a banana at this hour...."
Pinkie gets everyone with a really good zinger after Nyx is rescued.
Pinkie: You know what this calls for?
Everyone else[deadpan]: "A party."
Pinkie: Nah, we already got one of those downstairs. Geez, I was hoping one of you guys might have an idea for a change.
Pinkie's surprising reasoning for why Fluttershy can use cider as a G-Rated Drug:
Pinkie: "Now she gets that way if she even tastes something with multiple fruit flavors. I think it's a deeply entrenched psychosomatic reaction fixated due to her subconscious need for a psychological release for her repressed emotions."
There's so many things hilarious about the image of Luna dressed in a Whitney Houston-ized version of the Nightmare Moon armor, singing "Queen Of The Night" in the ROYAL CANTERLOT VOICE!
With Nyx, aka "mini me," singing backup.
Luna's Nightmare Night costume is basically Take That at Pinklestia. (Though Cadence seems to think it's aimed at her too.)
When Twilight's hoofmaidens try to teach Nyx and a visiting Bright Eyes how to properly enjoy tea and biscuits, the two of them decide to have a little fun by speaking in over the top upper class accents and bad puns.
Twilight's reaction to Spike's belching up over a dozen scrolls at once. (Also, the lengthy belch itself.) Topped off by Bright Eyes thinking of it as a Crowning Moment Of Awesome.
Celestia and Luna's royal guards trying very hard not to laugh, which probably feels like being the legionnaires in Monty Python's Life of Brian,
The repeated and hilarious Groin Attacks, in which Lord Blueblood ends up dangling by a chandelier by his, quote Luna, "Royal Lineage," and Prince Blueblood jumping out a stained-glass window and catching a flagpole in his Royal Lineage,
And though it didn't pan out, Ink Spot bursting into the throne room in Gryphon armor and challenging Blueblood to a duel, then terrifying him to the point that he jumped out a window was hilarious, combined with Share the Male Pain from every royal guardsman (and Ink Spot) in the room.
Actually, Prince Blueblood's paranoia the whole time is pretty funny.
Nyx enlisting Flitter's help to prank their class, thus breaking the ice and convincing everyone that she's still the same. Also a CMOA for preventing what could have been an angsty situation.
Pelé. Imagine an Hawaiian dragon version of Pinkie Pie, and you'll have a good idea of the lady.
Nyx's first meetings with both Dubloon and a young royal griffin.
Gossamer acting like a Genki Girl enough that Nyx resolves to check Pinkie's family tree and see if she's related to the Flutterpony.
Twilight's conversation with the lignomorph (a being of living stone), with it being completely oblivious to the fact she can't understand it. (Bonus: the Lignomorph's dialogue is all lyrics from Spike Jones' "Hawaiian War Chant.")
The kids accidentally taking a ride through Canterlot's drains.
Gossamer Logic Bombing the chief maintenance pony in charge of Canterlot's central clock tower, by pointing out the flawed nature of basing every clock in the city on this one, which is based on Celestia properly maintaining the day-night cycle.