In addition to the standard "characters are far different from their original characterizations for the sake of humorous juxtaposition" found in abridged series and similar web remixes, "Dragone Baby Gone" suggests that Rainbow Dash and Applejack got their Elements mixed up. This references a common joke in the fandom that they often (especially in the earlier seasons) seem to suit one another's elements more than their own.
Dragonshy may not be as evil as he's made out to be, seeing as how Fluttershy seemed more concerned about missed softball practices than being left out in the frozen tundra and being eaten by african ants that might not be able to survive in such temperatures. Considering her "element" is deception, it's possible she's lying to gain sympathy (that's not to say he wasn't abusive, but burning your kid's toys is a different kettle of fish than abandoning them in the wilderness).
Many fans interpret Cadance Notevil Goodpony as a Purity Sue based on her curriculum vitae as recited by Francis Sparkle. You'd be hard pressed to find any Real Life politician who doesn't strive to have a similar resumé.
Big-Lipped Alligator Moment: The entire Socker Boppers commercial in "Foaly Matripony". It shows up in the middle of the episode and has no relevance to the plot whatsoever.
Broken Base: While the series has had a very huge following in the MLP fanbase, in 2014 (helped in part by a certain member of the Analysis Community) it has picked up an equally huge hatedom as well. Those who hate the Witchcraft really hate it, and those who like it often refuse to even acknowledge the formers' existence. Even on this very wiki.
Crack Pairing: Twilight and "Francis Sparkle" (Shining Armor). Even if unrelated, they're still siblings.
Crosses the Line Twice: Their treatment of Raincloud, the Snooty Snark Evaders blinding Babs, the "Snowblind" segment and Twilight abandoning Cadence in a cave to die of dehydration in order to marry her brother.
Sweetie Belle, more commonly named Sweetiebot. Even or especially as a robot, people find her utterly adorable. She's oddly compelling thanks to her emotional depth and mannerisms. Even those who aren't fans of Witchcraft will still argue that she's a good character.
Silver Spoon and Diamond Tiara are far more popular here than they are in the show itself. Their valley girl accents and constant Lampshade Hanging make them genuinely funny as a parody of their arrow-straight Alpha Bitch characterization in the show. In the case of Diamond Tiara, this isn't saying much, but fans have really latched onto Silver Spoon, especially after Griffin created a spinoff series about her.
Fandom Nod: The Enterplay Series 2 Sweetie Belle card includes the line: "But her cutie mark acquisition program hasn't seen much success".
During "Sweetie's Big Race" in the fifth episode, Rarity and Sweetie Belle enter the chicken coop, which has "One egg per sentient life form" written on its side. They come out with a single egg because Sweetie Belle is a robot. This could also double as Fridge Horror, given what Rarity said about the Robot Police. Somepony knows something.
Also, Fluttershy initially doesn't want Pinkie Pie to sing her a song in "Dragone Baby Gone". But then all the sudden, she gets over her fears and jumps the cavern. Why? Because why wouldn't a girl upset about confronting her abusive father feel better after hearing about having both your parents die.
Why doesn't Applejack like Pinkie's song in "Cherry Bomb"? Because its lyrics ("When you're rife with devastation", "And your loved ones have been mangled", etc) are reminding her of the bomb.
Twilight acts in an explicitly horrifying way during episode 8, but not only has her nature been suggested in all the earlier episodes ("You wouldn't want to end up like Twilight's old friends in Canterlot, would you?") but Cadence remarks on the flat characterizations that Ponyville approves of. One wonders whether it's Twilight's doing or if it goesdeeper.
A newspaper mentions Newt losing a second eye and all of his limbs in a "baking accident". Perhaps Pinkie is not as sympathetic as one may think... For what it's worth, Newt's taking it in stride. "Now it's nap time ALL the time!"
In episode 3, we learn that Fluttershy is half-dragon (and all traits that make up a dragon are -recessive). What was the name of the episode they redubbed? Dragonshy.
Growing the Beard: The first episode is...not very good. Many of the lines are semi-random jokes that have little in the way of buildup, Jenny's delivery was a bit stilted and some character voices hadn't fully formed, the episode was relatively close to the source material, the funny asides from background characters were absent and they didn't speak, and it lacked the original music that would become such a strong part of the show. By the third episode character personalities and quirks began to jell, the voice acting quickly improved, a background score was added, and some of its first running gags began to pop up. By the fourth episode ponies were constantly chatting and lampshading jokes, the comedic timing was perfected, the plot strayed away from the source material with differing interpretations, and Pinkie's Brew became an instant hit, not to mention the introduction of Sweetie Bot.
Hilarious in Hindsight: So many elements from this series have turned out to be canon or at least similar to scenes that would appear on the show that people have wondered if Jenny and Griff secretly work on the show in some capacity, or get leaked info from people who do. Thus far:
In "Cute From The Hip", there's a joke about Apple Bloom earning a spinning cutie mark. In "The Cutie Pox", one of the cutie marks she got was a spinning-related one.
It also showed that Pinkie Pie's parents were gypsies and that she's been trying to carry on the family tradition. Cue a scene of her as a fortune teller in "It's About Time".
Twilight Sparkle mentioned having a brother in "Neigh, Soul Sister". She really does!
Speaking of Equestria Girls, Twilight's feelings for a certain blue-haired rocker boy is all the more entertaining now.
Even the parody song "The Convention" turns out to be eerily prescient — Rarity is said to have sewn her cosplay outfit "last night in [her] hotel room." Season 4 features an episode where she actually does that. Using stuff she stole from the hotel's own décor, to boot.
Their Equestria Girls parody trailer has a brief moment where Twilight says "Let's start a rock band!". Along comes Rainbow Rocks.
"For Whom the Sweetie Belle Toils" has Sweetie fall down stairs like a slinky.
In Rainbow Rocks, Twilight takes a while to accept Sunset Shimmer's hand after arriving back at Canterlot High, quite similar to "Horse Women" making an Overly Long Gag out of her taking Flash's hand.
Citizens of Ponyville must have dreaded the day Lord Smooze returned (aka the day the Friendship is Magic episode featuring the Smooze premiered). Taking it even further, Fluttershy, who serves as the leader of the Smooze cult, is one of the focus characters in said episode.
"Bloom and Gloom" features Apple Bloom having a nightmare about her family disowning her when she gets a non-apple related cutie mark.
After all the jokes this show made about how obvious it was that Apple Bloom would get an apple-related cutie mark, the one she actually gets does have an apple in it, but its meaning has nothing to do with that.
"The Cutie Re-Mark" shows the ponies in various actual wars...none of which have Applejack or Rarity on the front lines.
Rarity worries in "Cherry Bomb" that Applejack left them for better friends who paid for all the cable channels, and Fluttershy responds, "How will we ever compete with Noggin, or The Hub?" Now both channelshave been rebranded. (And MLP:FIM is one of the few, if not the only, Hub shows to survive the rebrand.)
Continued in "Cute from the Hip", where Apple Bloom claims that Fluttershy told her that Pinkie Pie has "evil gypsy powers and the voluminous hairof a temptress".
"Cute from the Hip" also heavily, heavily implies that Diamond Tiara has a thing for Apple Bloom, which she tries to hide by teasing her. Silver Spoon also wants to be more than friends with Diamond Tiara, but is aware of her feelings for Apple Bloom and spurred to jealousy.
It Was His Sled: Thanks to their memetic status, many newcomers will have already heard Pinkie's Brew and Gypsy Bard in their entirety, unaware that they originated from the series. Also, everyone knows the (at the time) hilariously unexpected twist that Sweetie Belle is a robot, again without knowing where she originates.
The constant debates of the show returning is seen as this. Due to the severe case of Screwed by the Lawyers, the show has yet to return. Judging from how both creators are busy doing other series, combined with YouTube having an infamously unbalanced copyright system and the fact that Hasbro is obligated to block episodes on a whim, this is sadly unlikely, at least for some. "When's the next FIW coming out", has been jokingly compared with Half Life 3 in redundancy.
Even as humorous as she is, Twilight is terrifying, especially in the eighth episode where she gets away with offscreen murder, and nopony seems to notice or care all that much.
"If the world isn't going to love me, then I'll teach it to FEAR ME INSTEAD!" Jesus Christ, Sweetie Bot!
In "Lunar Slander", Fluttershy is seen trying to duplicate Pinkie Pie's time portals with dark magic. She's interrupted by Twilight and Luna as they're trying to get her to socialize, while Fluttershy is desperately warning them that leaving the ritual unfinished could cause an unknown temporal disturbance. This goes unmentioned until the ending of the episode where Twilight writes to Celestia that she's relieved nothing scary happened. Cue an increasingly moody, and heavy remix of the ending theme that cuts to static, where we see Pinkie in her house. The portal reappears, causing strange shadows and distortions, evil laughing, and some sort of whispered chanting that builds in intencity until Pinkie is begging it to stop. Fortunately, it leads to something unexpectedly sweet for the orphan gypsy.
Several in "Gypsy Bard", such as "tilts it <-> resilient", "filly <-> city", "orphanage <-> wanna fit in".
"How Applejack Won the War" also has many, like "just wait and see <-> all we need", "farm <-> barn", and "battleship <-> honeycrisp".
Parody Sue: Princess Notevil Goodpony is a world-peace advocate, an organ donor, a childrens' book author, and the freely-elected leader of her own country. Being an Only Sane Mare unfortunately doesn't grant her an ounce of protection from the Crapsack World.
Snowblind: I don't want to accept the bad life I've been handed. From now on if I want something, I'm going to take it! I don't want to go to clown school, or end up as some lonely, middle-aged elementary school teacher; unfulfilled and wondering how I let my life get this way. I'm not some Christmas-special martyr, here to make you feel better about yourselves!
Spike. With his status as the show's number one Chew Toy, can anyone not feel bad for him?
Pinkie as well, given she's treated as a nut and a witch, as well as the fact her parents died. "Pinkie's Brew" is about her being so desperate to reunite with her parents that she's willing to fudge the space-time continuum to do it. She succeeded.
Rarity was screwed up pretty badly by the war, if Sweetie Belle's statement about how she spends every Veteran's Day is any indication. Not to mention the fact that she made a sweater that was specifically designed to hug her.
Luna/Molestia is awkward and lost and painfully aware of her loneliness.
Luna:[to the creepy statue outside Ponyvile] Oh statue, you are my only friend...
Raincloud. She never fit in with the ponies, and made a Heroic Sacrifice in her first and only appearance.
Cadence, the show's Only Sane Mare who has to deal with her soon to be husband going through Flanderization thanks to his sister's presence, and Twilight constantly trying to replace her as the bride. She succeeds, and leaves Cadence in the caves beneath Canterlot to die.