Twilight: Dear sweet Celestia! Discord, the god of chaos, has returned from his stone imprisonment to lay waste to everything and everyone we hold dear! Spike, we have only one option: We must locate the Elements of Harmony! Spike:(lights and smokes a bong) Yeah. Far out, dude.
Spike: She'd fuck anything. Chicks, dudes...didn't matter. Fat guys, skinny guys, guys who climb on rocks. Dogs, cats, squirrels, bugs. Snails. She fucked a snail. I watched her fuck a snail once. That sounds weird, right? Just hearing me say it? Imagine how weird it was to see it. She fucked. A snail.
Apocalypse How: Discord, Wolflor, the R-Dash 5000's, and all sorts of other natural disasters cause a Class 0 when they destroy Ponyville. Then Rainbow Dash pulls off a Class X-4 with her Sonic Rainboom. Fortunately, Rainbow Dash causes a Cosmic Retcon that prevents either from happening.
Balloon Belly: Applejack after eating tons of apples in "APPLE.MOV".
BFS: The Sword of the Holy Titans. Deconstructed in Ask Jappleack because, while powerful, there was no way for Jappleack and the Equestria Prime ponies to actually use it due to its size. Thankfully, Rainbow Dash becomes a giant to fight Discord in "SWAG.MOV", making her big enough to wield it.
Brain Food: In "SHED.MOV", Fluttershy threatens to eat Rainbow Dash's brain.
Brawler Lock: Between Discord and Rainbow Dash in "SWAG.MOV".
Broken Angel: Rainbow Dash loses her wings in the battle against Discord in "SWAG.MOV".
Call Back: In "PARTY.MOV", when Twilight tries to hold an intervention for Pinkie, she notices all her other friends are missing and asks Spike:
Twilight: This is supposed to be an intervention! Where is everypony? Spike: Applejack's in a coma, Rarity's being held hostage by Mexicans, Fluttershy's in the nuthouse, and Rainbow Dash is dead. Anymore questions, smartass?
The Cosmic Retcon in "SWAG.MOV" rewinds history to the very beginning of "SHED.MOV", well after the period Rarity is being held hostage by the immigrants from "DRESS.MOV". With her appearance here, she is completely fine, with no visible body damage or explanation how she escaped.
Cerebus Syndrome: A common trend in the series. "MAGIC.MOV" flanderizes almost all of the wackiness out of Twilight to turn her into a bland Straight Man, and "PARTY.MOV" turns Pinkie into a whorish celebrity addicted to parties. While this works on an individual level (each video uses a characterization that acts as an accurate parody of the character), this results in a bizarre case of one-man Depending on the Writer.
Chekhov's Gun: The Sword of the Holy Titans is mentioned in the Ask Jappleack blog by Twilight Prime, but she states no one is big enough to wield it. In "SWAG.MOV", the .MOV universe's Twilight summons it for a giant Rainbow Dash to use to finish off Discord.
Child by Rape: Apparently, Lyra Heartstrings is pregnant with twins due to being raped. She doesn't really seem to care about the rape part, though.
Spike: I think she said we're always welcome in her shed!
Continuity Lockout: "SWAG.MOV" features plot elements from the Ask Jappleack Tumblr, particularly the Sword of the Holy Titans, which Rainbow Dash uses to vanquish Discord. Applejack even explicitly references her adventures there.
Cool Sword: The Sword of the Holy Titans. Not only is it gigantic, it's powerful enough to One-Hit Kill Discord.
Cosmic Retcon: After Rainbow Dash destroys the universe at the start of "SWAG.MOV", the universe resets itself to the moment Apple Bloom gets her cutie mark, giving Rainbow Dash the chance to keep history from repeating itself.
Country Matters: A couple pop up during the series. In "PARTY.MOV", Pinkie even has it written on her shirt!
Crapsaccharine World: Everyone in this magical, colorful land of ponies is either retarded, a jerk, or completely nuts. Plus, we have slavery, cannibalistic psychopaths, and a giant monster who rampages through the city. Oddly for this trope, the authorities are quite competent, with police and doctors doing their jobs and taking matters seriously. It's improved a bit at the end of the series, since Discord's been killed (the other two monsters are Ret Goned in the process), Fluttershy's sane, and at least two of the Mane Cast have Taken a Level in Kindness. Applejack, after her Character Development, also resolves to start teaching others what friendship and compassion really mean to help make it a better place.
"Today is Hearts and Hooves Day. Meesus Rarity gave me a chocolate-covered heart. She said she found it outside Meesus Fluttershy's shed."
Dwindling Party: The mane cast gets gradually smaller as the shorts progress. As of "PARTY.MOV", Twilight is the only Element bearer still able to do anything. This is undone due to a Cosmic Retcon.
Early-Installment Weirdness: The episodes' plots mature over time, going from completely random, absurd, and even abstract in structure, to more straightforward, plot-driven, and comprehensible.
Earn Your Happy Ending: As surprising as it sounds, they actually do. After the resurrected Rainbow Dash performs a Sonic Rainboom and destroys the universe, she resets history to the point in time when Apple Bloom would've died (saving her life in the process). This also turns Rainbow Dash into a giant...somehow. In the end she beheads Discord with the Sword of the Holy Titans summoned by Twilight, not only saving Ponyville, but preventing most of the other disasters from ever happening at all. The ending has Ponyville rebuilt, the Mane Six on good terms again, and Applejack even keeps her Character Development from Ask Jappleack.
Everybody Lives: Well, aside from Derpy (who remains a decorative toaster cozy) and some innocent civilians (who lost their lives in Discord's rampage and battle with Dashzilla), all consequential characters survive in "SWAG.MOV" thanks to the Cosmic Retcon.
Extremely Short Timespan: From "DRESS.MOV" to "MAGIC.MOV", the series seems to take place within the course of one day ("DRESS.MOV" taking place in the morning, "SHED.MOV" taking place later in the day, "MAGIC.MOV" taking place at night, and so on).
Eye Awaken: Discord's severed head opens its eyes after landing back on ground. This isn't done for horror, because he's landed in Fluttershy's shed...
Feather Fingers: Parodied a few times. In "SHED.MOV" Fluttershy inexplicably gains fingers (which she snaps) for a moment. Even better, in "MAGIC.MOV", Twilight's hoof suddenly sprouts a finger for the sole sake of pressing a button; the same thing happens with Pinkie in "PARTY.MOV", who sprouts a finger for the sake of tapping on the bench she's sitting on.
Flanderization: Spike's stoner personality is based on three main canon concepts; the way it looks when he burns letters and sends them to Princess Celestia; a Running Gag within the fanon where certain frames appears as if he has "stoner eyes" (the middle of his blinking animation, where any character can look "stoned"); and of course, his scale colors (green and purple).
Freeze-Frame Bonus: In the Ask Jappleack blog, it is established that apples have their own system of letters, replacing the standard A-Z with different shaped apple symbols. On the bottom of Pinkie's vodka bottle in "PARTY.MOV", there's a sentence written in the apple's language. Translated, it reads "APPLE BLOOM NEVER DIED".
At a single point in "SWAG.MOV", when Rainbow Dash takes the Sword of the Titans, the words "THIS IS SO FUCKING RETARDED OH MY GOD I CAN'T BELIEVE I'M ANIMATING THIS" appear.
The penny Paco picks up in "SWAG.MOV" reads "In Twilus We Trust". Twilus, of course, is the leader of the Holy Titans who created the multiverse.
The labels on Pinkie's alcohol bottle in "PARTY.MOV", aside from the message in apple language, read "CAUTION!! EXTREMELY LAME freeze-frame gag", "WARNING! BOOZE — made from flowers or something I guess", and "Caution. Do not apply to open flame. Keep away from heat and open flame. Do not feed to babies unless you're really bored or something. I don't know. That might be funny I guess. A drunk baby. He would be like oh man googoo gaga I am so wasted I'm going to puke my strained peas all over my crib LOLOLOLOLOL."
Jump Scare: The endings of "SHED.MOV", "MAGIC.MOV", "PARTY.MOV", and the Panel Cartoons show Psycho!Fluttershy's Nightmare Face flying right at the screen. Subverted in "MAGIC.MOV", which gives off several moments where it looks like Rainbow Dash's corpse will suddenly spring up, but nothing happens.
Lying Creator: According to the description for "PARTY.MOV", "In this episode of the PONY.MOV series, Pinkie Pie tries to find a new dress in time for the Grand Galloping Gala. Meanwhile, Spike and Twilight finally make out, and the R-Dash 5000 learns how to duplicate himself." Only one of those (the R-Dash 5000 learning how to duplicate itself) is true.
Mondegreen: "Yeah, why don't you suck my dicknote tit you dumb bitch." Expect to see this pointed out once every hour in the comments.
Ret Gone: The R-Dash 5000 and Wolflor after Rainbow Dash's Sonic Rainboom does a Cosmic Retcon on Ponyville.
Ripple-Effect-Proof Memory: This seems to be the case with the Mane Cast when history resets itself after Rainbow Dash inadvertently destroys the universe, since they act as if everything that transpired between the reset point and the universe's destruction still happened.
The pony a coked-up Pinkie rants about music piracy to has a NERV cutie mark. This is a pony version of Garrett Hunter from Mega64, whose band "Slowdraw the Hungry Eskimo" was featured in the previous episode.
The Stinger: At the end of the credits of "SWAG.MOV", we see Fluttershy having tea in her shed (which doesn't appear to have any of the animal corpses from before) when Discord's head lands on it. He opens his eye to see Fluttershy glaring at him and saying "You're in my shed."
Rainbow Dash: Woah-ho-ho-ho, Applejack! You eat all those apples, you're gonna get a wicked bad tummy ache! (later) Pinkie Pie: Man, Applejack! You eat all those apples, you're gonna get a wicked bad tummy ache! Rainbow Dash: Aw, no way, I just said the same thing, you crazy cunt! Heheheh!
Time Skip: "SWAG.MOV" starts one year after Discord destroys Ponyville.
Took a Level in Jerkass: Spike in "SWAG.MOV". Though already a total Jerkass in his own right, he still seems pretty affable and only gets angry for good reason in previous episodes (such as Pinkie spraying him with menstrual blood in "PARTY.MOV"). Then Applejack returns, prompting a virtual "Who gives a fuck" from Spike, who then proceeds to verbally bash her when she tries to tell them about her adventure. Keep in mind that the latter was in a coma for five episodes, and barely did anything to provoke this over-the-top assholish behaviour from Spike.
Visual Pun: Selfish, greedy Rarity constantly talks about how generous she is. There are only two generous things about her in this show: her obese figure, and the beating she gets when her Mexican workers start a "revoluciˇn".
Writer's Block: Twilight struggles to write a letter to Princess Celestia because she hasn't learned anything, so she screws it up and throws it in the trash, which is full of other balls of screwed up paper. Not that Princess Celestia is even alive at that point...
Wrong Genre Savvy: Twilight's theories about ressurecting cadavers are all from movies, and she doesn't understand why they don't work. It's because the one dead body she tries bringing back, Rainbow Dash, isn't dead.