When the portal that transported Marcus into Prime!Equestria first opens up in Ponyville, Twilight, who can sense the massive amounts of magical energy it's releasing, remarks to herself that everything is tasting purple for a moment.
Once Marcus displays the powers of his enchanted rune tattoos, Pinkie Pie angrily screams, "HAX! I CALL HAX!!"
And what does Marcus say after his mind-sharing experience with Celestia, as he passes out? "I really like your mane..."
In Chapter 8, Spike's magical fire grows out of control and he and Pinkie Pie desperately try to find ways to put out the flames, only to fail each time. Even funnier is that Marcus and Lyra are oblivious to it despite it happening in the room with them.
In Chapter 11, after Celestia gives a very well deserved verbal smackdown on Blueblood, Discord laughs at Blueblood's attempts to glorify himself, leading the priss to run off scared. Marcus then sticks his leg out in Blueblood's way, sending him falling flat on his face.
Chrysalis and the Changeling elder Mythuselon argue amongst themselves when answering Celestia's worldwide summons. Luna gets annoyed and breaks out the Royal Canterlot Voice.
"Silence! Thou are in the presence of the Royal Sisters! As they say in these odd days, 'Shut thy wailing, wenches!'"
They then teleport Luna into the ocean.
Say what you will about him, but in "The Bigger Score", Trevor Philips hangs a neat lampshade on the inherent absurdity of the story's premise:
Trevor: And another thing! When I thought of the end of the world, I imagined big ass fucking meteors, or the Earth deciding that she had had enough of our shit and would just blow the fuck up. Never thought the apocalypse would come in the form of pastel ponies!
Right after a touching and loving reunion, Marcus tells Cheerilee that he'll stick around in Prime =!Equestria for a little while to gain better control of his runes and help train the Royal Guards to be better prepared for the war against their TCB counterparts. Cheerilee then tells Marcus, "You better not mess around with my twin, okay? Just because we are the same pony doesn't mean it counts."
'Sons of Legacies (Part 2)' gives Discord an opportunity to let out the snark in almost Dr. Venture-esque form.
Sombra: Hee hee hee hee... you walk into the domain of my toy, Discord! All of your magic amounts to nothing in here!
Discord: You were not held enough as a foal, were you?
Sombra: You will never understand, I gave my entire being to Luna and she turned me away! I did everything to extend my life and they were all failures! She cast me aside once she learned what I was doing! After the war, she sent me away to take care of her foolish grandson! I will have my vengeance!
Discord: You know... Your life story is so cliché it's almost boring.
'Sons of Legacies (Part 3)', though it starts out pretty damn dark, eventually goes the opposite route of the infamous chapter "For Whom The Bell Tolls" and descends into the most hilarious and Reference Overdosed absurdity the writers can come up with.
Discord uses his powers to go all Looney Tunes again by summoning a number of characters into Marcus' Mental World. One of said characters is Mr. Torgue, who does a characteristic guitar solo with his mouth while shooting Newfoals, and headbutts a Newfoal's skull so hard it breaks. The most bizarre part of it, however, has to be when we see Discord conjure a hand-puppet of Rarity to stare down a mental projection of King Sombra, who had been disguised as Queen Celestia thanks to the disguise literally getting beaten off of him, not only does it looks like he's cross-dressing, but that he's wearing bad plastic costume jewelry. Upon spotting this, the hand-puppet of Rarity yells, "SWEET CELESTIA! KILL IT WITH FIRE!" while Discord is plainly moving his lips.
Word Of Fluffy is that he was kidding, though he's debating whether or not it's canon.
Stephan, initially wondering how to train the dragons, reassures himself by comparing them to war elephants. Then his brain starts getting giddier and giddier about flying war elephants, "aerial APCs that can carry troops and spit fire!" which all ends in "oh this is going to be AWESOME!"
Chrysalis turns herself into Celestia for a joke, only for Luna to spot its flaws at once and scold her because... "My royal sister has nowhere near such a trim posterior!"
Lyra's human porn stash, as well as her reaction to Bon-Bon being okay with a human and two pony threesome.
Although 'Reveries' is a fairly somber arc, coming off of "Pale Moonlight", it has a few funny moments.
Chrysalis is a complete troll from the onset, starting by warning Stephan that he might turn up naked in the dreamscape (he doesn't, and there was no chance of it, either), making her entry in the dream relaxing at a pool on an inflatable raft shaped like Shining Armor, and then, well, there's her method of dealing with the projection of the Blue Spy. Complete with the moment after when she spits out the remains of the domino mask.
What adds to this is the Blue Spy's Curse Cut Short right before Chrysalis pounces on her. It's funny because it's the only instance of cursing within the chapter, for a story which is not typically shy about foul language.
Yon-Soo thinks to himself how the little pegasus filly he and his friends rescued, Comet Tail, is so adorable she's going to give him diabetes.
Comet's mother, Aquamarine Glimmer, reminisces on how she learned shield spells (one of which she used to protect Porter earlier on) because Comet would always whizz past her.
Aquamarine: "I had to get her off the fridge so many times... and most of them were before she could start using her wings."
According to Fluffy, this is a based on a true story - his uncle managed to get on the fridge when was a child, somehow, and nobody in his family knows how it happened.
The group having themselves some fun in a truck they swipe, Melnik getting sloshed and singing stupid songs with Comet, and then Melnik collapsing on top of the HLF members they captured.
In "A Journey to the East", we get to see a clip of Yon-Soo's TV show, "The Baker's Dilemma". Kizuna Tallis states that she and Doctor Fluffy were laughing as they wrote the scene. Doctor Fluffy, however, remembers them trying to out-ham each other.
Calm Before The Storm
The reveal in Chapter 2 of Calm Before The Storm that Big Mac gave Diamond Tiara food poisoning when she called Applebloom the product of incest. On top of that, Doctor Fluffy claims that he only let Redskin write Big Mac's portion of the story if he kept in that one line.
Dark Kraber: Vengeance is mine. Beyond that, there can be nothing else - there should be nothing else. But I remember a time when I thought there could be.
And I remember you.
You were the voice that told me to become horsefucker. That made me suggest some level of innocence. Called me a chopkont.
You are young, and you are naive. I have stood where you are now. I lost what you have lost. And I have seen and created horrors that make the worst deeds you've done seem like nothing - you know this.
You're wrong, Viktor Kraber. You're wrong to doubt the path you walked before now. Your purest purpose was vengeance. You are the slayer of the Reaper. In time, you could be more - you could be the man who kills Pinkie Pie. You could be a slayer of God-Tyrants.
Do not fool yourself into thinking you can find atonement. Forgiveness is a lie. No matter what you do, you will find no forgiveness. You will find tolerance at best, and they will treat you as a tame attack dog. Is that what you want? Is that what you think you deserve?You could be a God-killer. You could be more than you are. Do not turn away from rage. Embrace it! Use it! You know who your enemies are. DESTROY THEM! There is nothing else, Viktor. For what we have lost, let there be no forgiveness, no pity, no mercy - only death, only death! Only death! ONLY DEATH!