Funny / The Elements of Harmony and the Savior of Worlds
Celestia's reaction to Twilight Sparkle's letter mentioning Megan. She's calmly reading the letter while sipping some chamomile tea, then when she gets to the bit about Megan, cue her dropping her tea cup and doing a Spit Take into the face of her minister of commerce.
Celestia:WHAT THE FLYING HERD?
Luna has the exact same reaction when Celestia shows her the letter. And this time, the Spit Take is in Celestia's face.
Megan meeting Lyra.
The reveal that Megan's young daughter Michelle somehow tied a big purple bow around the base of Twilight's tail without the unicorn realizing it.
The Embarrassing Foalhood Photo of Celestia, after discovering a music act on Earth, with her mane dyed black, thick eyeliner under each eye, heavy chains around her neck and fishnets on all four legs. The accompanying flashback is also hilarious.
Celestia stomped her hooves and growled. "Magic Star, Wind Whistler, you don't understand!" she cried. "The Cure is my life! They speak to me and my soul…"
Twilight spends the night at Megan's house, and the next morning we see that Michelle has literally covered Twilight's tail in bows and ribbons and braided her mane. She's understandably a little freaked out.
Michelle: Too much?
When Celestia realizes she completely forgot to tell Megan and the others about Cadence, she face hoofs so hard she causes a minor earthquake. One that manages to wake up Trixie, who's in a town several miles away.
She follows up on this by introducing Cadence to Megan in an over-the-top manner; Cadence comments that she makes Luna look modest by comparison sometimes.
In the first chapter of Side Stories, we have Twilight completely geeking out over Optimus Prime, especially how his trailer disappears when he transforms. Then when he leaves, he explains that even he doesn't know where it goes.
Cadence face hoofing at how unsubtle Mike is in his attempts to hook up Fluttershy and Big Mac.
Also, her calling Shining by his apparent pet name "schmoopie-doo" in order to get him to stop prostrating to Mike (who, as Megan's husband, he's treating like divinity).
Twilight's momentary Freak Out when she remembers Michelle brushing her.
Rarity freaking out over trying to make a Gala dress for Megan.
Danielle and Michelle's surprise at Rarity singing at one point.
Danielle's eyebrow quirked. "Wait, is she singing?" She looked down at Dinky. "Why is Rarity singing?"
Dinky shrugged. "You get used to it."
Sweetie Belle once again causing a mess in Rarity's shop. Megan says that the incident earlier in the story with the tree sap makes sense now.
Twilight spitting her soup all over Shining Armor and Cadance when they tell her about their engagement.
After Spykoran the Old shrugged off Fluttershy's Stare, she inexplicably fainted.
It would seem Twilight learned how to dance from Celestia. Picture that for a moment.
After Megan said "Cross my heart and hope to die, stick a needle in my eye!" The ponies and Spike were disturbed by that saying. Especially Rarity, "What an awful saying! A needle in the eye? How ghastly!", then she faints, over-dramatically.
When Danielle and Mike express shock at the sudden singing at the Gala, the latter tries to say something, only to suddenly start singing himself, to his shock. Afterwards, he asks Danny how he coped with it back in the day.
"I used a lot of throat lozenges."
In the Side Stories "How Christmas was Saved... Sort of", we find out that Megan (drunk from eggnog) was telling the story.
Twilight Sparkle: And you're cut off before you tell us how the Dinobots saved Easter!
Cobra Commander's origin: before COBRA, he was a used car salesman.
This was actually taken from his Marvel Comics backstory (RK-Striker admitted that he mainly based CC off that version); in "Day of the Broken Fang" he says that his cartoon backstory was invented by Cobra-La when he stumbled upon them while traveling the Earth.