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 re-shelve 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.
Chapter 15 involves, before the CMOA with Night Light and the reporter, an adorable scene with Bright Eyes "petitioning" Princess Cadence if Nyx can come out to play. Ending with this moment:
Princess Cadence (after Bright Eyes leaves to go to Nyx and the little foal's room): "I want one."
Shning Armor: "As you wish. Shall we shop locally or mail order one?"
Cadence discreetly slugs him in the shoulder
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!
Waldorf entered the room with a tray to retrieve their glasses. "A Mister Roller Reel to see you, Miss," he said smoothly to Twilight. Right behind him came the scruffy teenage pony, camera mounted on his shoulder and saddlebags stuffed with film cartridges slung over his back. "Hey, Miss Twilight, I'm sorry I'm la—- wuhohoah." Roller came to a screeching halt.
It has to be kept in mind: Roller Reel was a colt. He was a teenage colt, one who had spent the early portion of that awkward stage not at the beach girlwatching or at school dances flirting with the local cheerleader fillies, but hiding from the press gangs in the basement of his home and slaving in King Sombra's mines. Fillies, in brief, had been less of a part of his life and more like a distant dreamlike concept. It had been intimidating enough working under, as a subordinate, to the rather pretty protege of a Princess.
And now he had, without warning, walked in the middle of a room filled with what were routinely regarded, by those that commented on that sort of thing, as six of the hottest young mares in Equestria. He took one sweeping look at the roomful of beauties, heard their friendly 'helloes', and felt an emotion flush through his body he'd never felt before.
He gave them his suavest smile and smoothed his mane back. "Hey, ladies," he said, threw up an elbow to lean on the back of Twilight's chair, missed entirely and fell flat on his face at their hooves.
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!!!
Upon finding Level Head's tomb, Twilight starts reading the journals that describe the true Hearthwarming Day story. At one point in the story, Level Head starts discussing how his grandchild had a threesome with two of the other major figures in the story. Twilight then mentions that somebody had scribbled out the juicier details and written LIES, ALL LIES over it.
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 tadů
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.
When Twilight accepts Ink Spot's proposal, Nyx hops around the room "like Pinkie Pie on triple espresso."
Nyx: "EEEEEEEEE! Omigoshomigoshomigoshomigosh!!"
Actually, Prince Blueblood's paranoia the whole time is pretty funny. Especially his Oh Crap! moment upon seeing Celestia transform from getting angry because of Duke Blueblood insisting on the Arranged Marriage contract.
Prince Blueblood: "Oh no no no! Not the fiery mane of doom again!"
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.
Princess Luna's tongue lashing of Triton for making poor Nyx believe she killed hundreds when she caused Eternal Night in the original story. Very much needed after Nyx's emotional breakdown.
Luna handling the Unresolved Sexual Tension between Celestia and Triton by throwing a potted plant at his head and spelling out how Celestia feels about him.
The Mane Six's reactions to finding out that the planet is a starship.
Rainbow Dash (After finding out about the planet being a starship): How fast are we going?
Twilight: Rainbow, that—
Rainbow Dash:Come on, how fast??
Twilight (rolls her eyes): About 92,000 miles per hour, Dash.
Rainbow Dash:Holy horseapples!!!
Also Rainbow's yell of "FAR FREAKIN' OUT!" when Twilight first states this fact.
Pinkie and her reaction to finding out that she essentially missed five of Twilight's birthdays.
Pele: Oh, rule de worl', eh? Joo tink mebbe we were all gon' sit on our tails and let you rule?
Luna giving Celestia a zerbert.
Nyx finding out that Songhili is the Selkie king, and his proposal for a water-slide transportation system for his people.
How Celestia reacts when she figures out that Twilight Sparkle's "Marriage vows" are actually a garbled spell, and she's about to trigger a massive spellsurge in a room full of epic magic artifacts and nigh-cosmic entities. It ends up turning Ink Spot into an alicorn!
During Spike's beatdown of Tirek, the dragon engulfs the tyrant in green flames.... which sings off his beard and sends it to Celestia, in Tartarus.
Tirek: (noticing his beard missing) MY BEARD!!!!!
Meanwhile, in Tartarus, Celestia and Luna are chained. A ball of hair falls from the sky, burying them two.
Celestia: (buried under Tirek's beard, half-muffled): Okay. Chained to a peak in Tartarus is bad enough. This is disgusting.
Luna: (gagging) Forsoth. Ye gods.... the SMELL.... Doth Tirek never BATHE?
Heartwarming and Funny moment for "Now Wouldn't That Frost Ya": Flitter's first encounter with the Cake Twins. Pumpkin thought Flitter was injured, so she brings a first aid kit and patches her up. She almost melts from the cuteness.
When Willow's scaring of Snips and Snails is revealed, Cheerilee doesn't believe them...until Willow demonstrates what he did. This goes on for several minutes and Scootaloo asks him to do it again.
The end of "A Little Hearth Warming" is insanely funny. Nyx, being a classic little kid was worrying about Santa not coming because of her nature. Then at the end she says, "Aww, man. This night is gonna last FOREVER!" Now if you remember whoshe is, you will find out the joke.
Twilight certainly finds it hilarious, laughing hard enough to fall out of bed and wake her husband.