When Twilight's book is telling how Princess Luna transformed into Nightmare Moon, the illustration suddenly goes from Luna's eyes closed in sadness to Nightmare Moon's eyes open in utter hatred.
The Ursa Major that was seen at the end of Boast Busters. The way it's a grotesque mix of at least two creatures that are terrifying on their own is petrifying.
The Ursa Minor as well. It's big enough to destroy Ponyville in a matter of minutes, lives in a cave in the Everfree Forest right next to the town, and all it takes to wake it up is two young, curious ponies stumbling into its cave. Trixie's reaction to hearing it was only a baby is very justified.
How about the first time when Fluttershy was so relieved to have found her friend, she starts talking to her, and then BAM. Realizes she's stone. That's just about the scariest thing. Even scarier, if you recall Discord after being freed from stone, he could see and hear everything from around him. It must be the saddest thing in the world to have a friend worry about you in which all you can do is watch. This should be labeled in And I Must Scream
Try listening to the background music with headphones on as the Crusaders enter the forest.
The way the Cockatrice itself rises up out of the bushes is quite unnerving.
Though on the bright side Zecora who lives in the forest 24/7 probably has potions to cure being turned to stone on hoof at all times just in the off chance she runs into a Cockatrice. So if Fluttershy had failed, Zecora could possibly have been able to reverse it.
The Show Stoppers
The Cutie Mark Crusaders getting caught on Pinkie Pie's candy machine in "The Show Stoppers" is really frightening, especially with their bodies disappearing in the rainbow goop and only the Eye Scream left visible. They came out intact (albeit sticky) but still.
Becomes more horrifying if you happen to have listened to (or read the fic version of) "Rainbow Factory".
A Dog and Pony Show
The first time the Diamond Dogs show up, hiding in a bush and talking in a Gollum-esque voice and you have no idea what they look like.
The Cutie Mark Chronicles
A lot of fans were creeped out by young Twilight losing control of her powers in "Cutie Mark Chronicles". She is writhing and twitching inside the bubble before Princess Celestia comes and calms her down. She was in pain. Let's just be glad Celestia came when she did.
Her parents look of terror right before they're turned into plants is bad enough, but after they revert to pony form, they look downright horrified. At least they recover fairly quickly.
Party of One
Pinkie Pie temporarily going nuts in "Party of One" was legitimately spooky, bordering on pure terror. The odd expressions and the violent spasms make it worse. The creepiest part is, after they say that it's her birthday, she is just to normal, like it never happened.
Pinkie was starting to hear voices in her head, and believing they were coming from inanimate objects, signs of schizophrenia (and Funny Schizophrenia is averted as much as possible on a kids show). After one day of being alone. Still not bad enough? The voices in her head were telling her that her friends were losers and she shouldn't speak to them ever again.
It's bad enough when you see the build-up. Put yourself in Rainbow Dash's shoes for a second. This is one of your best friends, and you go to get her for a surprise party. You expect her to be her usual, cheery self, and instead she's... Gone crazy. Not the fun kind of crazy she usually is, but scary crazy. You don't know what happened, but your best friend is suddenly not herself, in a very disturbing way. And she's replacing you with a bucket of turnips that she thinks is talking to her. How do you react to that?
Fans have left comments on Youtube saying they believe this episode inspired the infamous Cupcakes. (In actuality, this episode was written beforeCupcakes was written, but aired after said fanfic was released.)
While Rainbow Dash is fleeing from Pinkie Pie, she hides inside a bell at one point. Then you see two eyes... on the clapper. It's Pinkie Pie as the clapper.
"The Return of Harmony", part 1: When Discord first begins to awaken, we see his heart beating inside of his stone-cold prison, with a black aura pulsating in and out of visibility each time the heart beats.
Discord gets up to some pretty disturbing antics. Robbing unicorns of their horns and pegasi of their wings, brainwashing Twilight's friends into becoming the opposite of their true nature, tricking Rainbow Dash into abandoning the game with a vision of Cloudsdale being destroyed...
Although it's not dwelled upon, the taking of the wings and horns has some Body Horror implications. Imagine having a couple of your limbs vanish.
Rainbow Dash's encounter with Discord gets even creepier when he produces a box that he claims contains her wings. Granted, we don't see Dash open it, but the idea that her unattached wings could be just sitting there inside a sparkly, neatly wrapped gift box adds new levels of unsettling to Discord's antics.
Worse still, they obviously aren't bloody and hacked off, since they were removed via magic. So we have two detached wings, in a box, just lying there as if fake.
Pinkie Pie's Mind Rape is probably the creepiest of all, with demonic balloons laughing at her and circling her while she begs them to cease.
Even worse when Discord removes his head so his talking face is on the balloon. The faces of Pinkie's friends showing up on the balloons too is unsettling at the very least.
Fluttershy's forced Mind Rape was probably the worst of all, it looked...painful.
The others suffering from Mind Rape is rather unnerving as well, not only did Discord reverse their personalities but metaphorically raping them as well.
The animals with the long spidery legs at the beginning. They just look... wrong.
The worst part of it all is Discord's Faux Affably Evil personality. It's just so... disturbing. He loves what he's doing to them. He loves performing Mind Rape on the mane cast and he didn't even need to do the mundane version; as he showed with Fluttershy, he could've skipped straight to the instant supernatural kind. He did it because he wanted to. No wonder Celestia and Luna imprisoned him instone for eternity!
Not only that, this shows that he's not even trying, and yet he still won! Who knows what he's capable of when he starts getting serious?
And to think that he ruled Equestria before Celestia and Luna came along and turned him to stone with the Elements of Harmony.
Another bit worth noting is part of the stained-glass window with the puppetmaster Discord. Him controlling the strings of the obviously-in-pain ponies is creepy enough, but then you notice he is dangling the ponies above a pit of fire. Do we even want to know what happened there?
Those who study Tarot would definitely see the resemblance between this image and the Devil card from most major decks; the ponies being "chained" by the puppet strings, Discord's somewhat goat-like face, even the pit of fire bit can be found in the standard variants of this arcanum.
The Return of Harmony: Part 2
The way Discord is defeated. He writhes in pain as he is turned to stone. Afterwards, the statue falls to the ground, the camera showing a close up of his horrified face.
Discord's World of Chaos was getting progressively worse by the minute, and he only ruled Equestria for a few days max. With what was implied the previous episode (Ponies being held by puppet strings over a pit of fire along with pained, horrified screaming), it's a very good thing they stopped him when they did.
Discord: And these are only my first changes!
The "slender bunnies" are freaky enough, but if you look closely when they stampede across screen before the final confrontation with Discord, it looks as if they don't have eyes.
What made Lesson Zero so effective was how much it played with our expectations after The Return of Harmony. For instance, who would've expected any of this?
On the inverse, some people found it scarier because it came after "The Return Of Harmony" and it made it seem like Twilight was psychologically damaged by Discord.
For starters, quite a few people found Twilight's mental breakdown to be more than a little unsettling. Also, she seemed to have the power to brainwash ponies. She literally managed to cause all of Ponyville to descend into chaos just with one spell.
The spell also seems to make ponies eyes roll back into their skull rather slowly.
Fluttershy apparently breaking a bear's neck. It turned out she was only doing something chiropractic on it, but it looks horrific at first.
Spike's claw cramp. It looks like he has a grotesquely broken wrist, and the sound effect doesn't help.
The short moment where Twilight notices a few fillies playing jumprope, then she imagines them laughing at her, in an almost literally hellish background (see the page image).
There is an extended version out there. Sweet dreams, little girls!
Zecora telling the fillies about Nightmare Moon. She blows some green dust and illusions of Nightmare Moon appear, looking very vicious.
Princess Luna's actual entrance. She flies in with two grim looking ponies, with lightning flashing in the background, making her look pretty intimidating.
This is part of the conflict for the episode—as it turns out, one thousand years ago, the standard royal etiquette was to be intimidating.
After Pinkie Pie's third misunderstanding with Luna, the princess brings all the fake spiders to life! Which immediately overwhelm one of the ponies, knock her down, and crawl all over her. To anyone who has arachnophobia (or just doesn't like spiders), this is the creepiest part of the episode.
Luna finally gets furious after spending the whole episode being treated like a monster, complete with Glowing Eyes of Doom and summoning an ominous storm out of nowhere! A good lesson on why ticking off a Physical Goddess is a very bad idea!
Apple Bloom appears to have been on the verge of dying of exhaustion.
A ponified Jesús Quintana in the same building as two groups of foals!
May The Best Pet Win!
While the Mix-and-Match Critters of the pets in Rainbow Dash's dream aren't that scary and are actually kind of cute, having Opal coming out of its mouth is truly frightening.
It does not help matters that Opal in that scene reminds some of Charlotte.
The Quarry Eels. They aren't particularly monstrous, but damn they're fast, and not one of Dash's prospects manages to avoid being chomped. This doesn't stick (the bat pulverizes one from the inside out), but they lair in otherwise normal holes in the wall, and they give no hint to their presence.
Sweet and Elite
This episode features a split-second closeup of a Salvador Dali-esque painting of ponies being horrifically stretched and melted. And Rarity approves of it!
The Secret of My Excess
Spike's display of his nictitating membrane after Twilight leaves him be can be creepy to those unfamiliar with reptilian biological mechanisms. We've come to accept these characters as humans rather than animals like they really are. This scene is similar to watching someone you know as being as human as you are slowly turn into something not human.
While grown up dragons in the show have a generally cool appearance, Spike's grown up form looks more menacing than the ones in "Dragonshy" and "Owls Well that Ends Well".
Hearth's Warming Eve
The Windigos. Ghostly horses that feed off of negative feelings and distrust. The blizzard they caused further fueled the emotions that fed them. Close to the end of the episode, their cold became so intense that it froze the leaders of the three tribes alive, right where they stood. And apparently, they're still around, meaning that if you ever let your negative feelings get the better of you, they'll be waiting.
The scariest part is when we first see them, there's nothing explained about them. Until the end, we have no idea what they are or what they're up to.
The moment they first appear... the camera zooms out past the cloud layer and we see these huge horse-like creatures with flashing eyes neighing loudly and clearly causing the giant, kingdom-destroying ice storm.
It gets better with research: they're either named after an Algonquin legend of evil spirits that could enter people and turn them into cannibals, or after Ithaqua the Wind-Walker, also known as the Wendigo: an Eldritch Abomination also known for causing horrible, deadly blizzards, and a character from the Cthulhu Mythos. Now that is a Shout-Out the original primary demographic is unlikely to get.
Family Appreciation Day
The Timberwolves, a very eerie design of wolves made of wood. Actively malevolent, and practically immortal (regenerative abilities) to boot, it's another rare time on the show where Talking the Monster to Death won't work.
The "signs" that Granny Smith is on the lookout for, when they haven't been explained, can be a little unsettling. The Timberwolves' howling, the ominous weather, the crows and ravens forming symbols in the sky... it feels like Black Magic rather than an apple harvest.
Even after they're explained, there's still something terrifying about a ominous storm coming out in the middle of an average, sunny day while crows squawk and winds that come from nowhere blow the leaves aside to show the apples changing color.
The scene where Pinkie Pie is searching frantically for the twins after putting them to bed looks like a scene out of a horror movie. She finds Pumpkin Cake (the filly) in a closet, chewing on a rubber chicken in increasingly-more-jarring slow motion. She goes out into the hallway to find Pound Cake (the colt). It's dark, the curtains are blowing, and there's weird music playing and she keeps hearing Pound Cake's laugh everywhere. It brings to mind some of the horror stories about babysitters alone in the dark...
That scene was filled with references to horror movies, so it's only natural it would be scary.
The blowing curtains also imply that there is an open window somewhere, and Pound Cake has just started flying. And the Everfree Forest is never far away
Well, considering that scene was directly lifted from the "dead baby crawling on the ceiling" scene in Trainspotting, it's naturally horrifying.
There's also a massive amount of Adult Fear in that scene. Taking care of a child and then losing them is one of the worst feelings ever.
The entire Daring Do story is quite shockingly violent for this show. The worst is definitely when she's tied to a slab in a room filling with sand and spiked walls closing in, while spiders and cobras crawl over her.
Ahuizotl's introduction. It's not immediately apparent how off his anatomy is until he starts talking, and when he does, it's in Pinkie Pie's voice, which is immensely jarring.
which says nothing about his real life origin: 
Hearts and Hooves Day
Apple Bloom's Imagine Spot about Ponyville sliding into chaos without Cheerilee teaching and Big Macintosh helping at Sweet Apple Acres is amusing, but it also features a disturbing shot of a severely-emaciated Lily.
A Friend in Deed
It was somewhat unsettling to see Pinkie Pie squeeze one of her eyes through the keyhole of a lock.
Because Nightmare Moon, Discord and the Windigos aren't bad enough, Cerberus apparently guards a gate that holds all manner of evil creatures, and there's nothing stopping him from running off whenever he feels like it. Not only that, but according to Twilight the place is Tartarus - which was more or less Hell in Greek myth, as the lowest region of the underworld where the souls who received punishment were sent. Given that Cerberus guarded the underworld in Greek myth, and the MLP production team has snuck quite a few mythological references in, the fact that we're more or less introduced to Hell is unsettling in itself.
The ending of the first half. Specifically,thelast20-oddseconds. Seriously, the only thing that kept fans from freaking out completely is the fact that the second half of the plot started almost immediately.
To some, Celestia's final line can be pretty unsettling. This isn't simply disappointment like back in Lesson Zero. Its clear that Celestia is enraged by Twilight's apparent screw up.
A Canterlot Wedding Part 2
When Chrysalis unravels her Cadance disguise, there's a short bit where, for a second, she has an Eyeless Face, and then her eyes suddenly open with stretched out sclera. This is then followed by an Evil Laugh with an extreme close-up of her face◊. Yikes.
The shot directly after that, when her shadow falls over Cadence, looks absolutely terrifying!
Celestia finding herself trapped in a chrysalis.
The moment where Twilight was trapped in the abandoned mines of Canterlot, and Chrysalis!Candance showing herself on the crystal walls, taunting her and telling that Nopony would ever find her... Also her face when she reveals herself to Twilight!
Many of Chrysalis's expressions while disguised as Cadance, notably her crazed looks during "This Day Aria".
For those with trypophobia (the fear of clustered holes and/or holes in bodies), her limbs and horns can be downright horrifying, on top of her already-unnerving appearance, she just looks downright wrong.
Those with entomophobia and how the changelings looked like a hybrid of a pony and a housefly.
Queen Chrysalis revealing her true form. Especially the spot directly afterwards where her shadow falls over the real Cadance. The shadow seems specifically intended to make her look as terrifying as possible!
Has anypony ever talked about Chrysalis's voice? I know it's an edit, but just... that low, unnatural, almost insect-like moans that sums up her voice pretty much keeps you up at night, if you give it much thought...
The Crystal Empire Part 1 and 2
King Sombra is one of the more terrifying villains in this show.
The reaction of the Crystal Pony Twilight talks to when thinking about King Sombra. The way she says she doesn't want to remember King Sombra's reign involved outright slavery and was so horrible that Celestia and Luna intervened, turning him to living shadow and sealing him in ice for eternity. Keep in mind this guy is a unicorn, not some Reality Warper like Discord. Just what kind of monster is this guy that the Princesses were more thorough disposing of him than they were of a villain whose Evil Plan was World Gone Mad?
King Sombra's lack of a backstory adds more fuel to the fire. Who is he? Why is he so obsessed with the crystal ponies? How did he become so powerful that it took two God Emperor level princesses to seal him away, and even then it wasn't enough to stop him?
He's the only antagonist to not get a chance at redemption.
More terrifying than anything else is his Dangerously Genre Savvy. The Crystal Heart is the one thing, aside from direct intervention from two god-like beings, that could stop him. What does he do to prevent others from getting it? Aside from making everypony who knew about it forget it existed and removing any record of it's importance, he put defenses around it. What kind? First, he puts it in a secret passage that a spell only he knew could open. Had Twilight not seen that spell from Celestia, it would be impossible to reveal. Second, he puts a door in the way that, if the same spell is used to open it, traps the intruder in a nightmare that is inescapable unless someone else wakes them up and the door itself is a jerk and will toy with anyone who tries to enter it. Last but not least, at the top of the tower where he hid the Heart, there's a spell that, when triggered, traps the intruder in a barrier that will pull the victim back in if a teleport spell is used. More importantly, it tells Sombra that someone has reached the heart. Unlike some villains, he took every reasonable step to ensure that no one could get the one thing that could stop him, since it couldn't be destroyed (said object having the power to aid him in conquering the world probably has something to do with that). Not bad for a villain with only a couple of minutes of screen time and very little dialog.
The stairs; hundreds and hundreds of stairs. After climbing down an absurd number of stairs, anypony after the heart would then have to climb up even more stairs to reach it. So, anyone who tries to claim the heart will be exhausted by the time they reach it, and unless you recklessly jump off the top of the tower like Spike did, the only way out is going down, then up, those stairs again. By the time you get there, Sombra would be waiting for you at the entrance, because his spell would tell him you've taken it. King Sombra takes Crazy-Prepared and Dangerously Genre Savvy to new and frightening heights. The only reason he was defeated was because Spike didn't listen to Twilight and went after her.
He made a door that leads to your greatest fears and brainwashes you into living out your worst nightmare; Mind-Control Eyes and everything.
When Sombra is breaking through the barrier in bits and pieces, dark crystals start growing up out of the ground and closing in on the ponies, trapping them in the centre of the empire and there's nowhere to run.
Twilight's worst fear.
As Twilight opens the door and it reveals Canterlot, rather than a part of the Crystal Empire, the way Celestia treats Twilight surely would creep everypony out!
The wall had one of those mosaic's that depicted Equestrian history. What did it depict? Sombra winning! Not only is it frightening in just the idea, but the imagery is truly frightening. Looking closely, it had Twilight hurling down onto crystal spikes that are engulfed by a pit of flames while a truly terrifying depiction of Sombra looks on. He most certainly outdid Discord in the 'horrifying things depicted in stained glass' category.
Spike's worst nightmare. We don't see, but we can hear it, and if it's anything like Twilight's, it was horrifying. What was it? Twilight dismissing him because she no longer needed him. Less than ten seconds, and he was brought to tears by it.
As the episode progressed, the field began to flicker back and forth as Cadance loses strength. It shifts between serene blue and hellish orange, reminding the audience that Sombra is right outside waiting for it to fail so he can retake his kingdom.
Then at the end, when it does fail, the Crystal Ponies are instantly terrified at the realization that King Sombra's returned. One of them has a Freak Out from the simple realization Sombra's back and runs for her life... right into King Sombra himself who gives her a Slasher Smile. The tone in which she says his name is one of complete and utter fear. This scene isn't scary because Sombra's in it (though that is scary), it's the sheer terror he's able to inspire in his slaves.
Unrelated to Sombra, Pinkie Pie is revealed to own skintight suits of her friends. Fluttershy, for one, is visibly disturbed by this development, especially because Pinkie was wearing a costume of her.
Too Many Pinkie Pies
Similarly to "Lesson Zero", the thing that made this episode so effective was how it blew our expectations away. It was advertised as a very silly and lighthearted episode and it was! Until the climax.
Twilight dispatches the Pinkie clones by zapping them with magic that inflates them into bizarre fleshy balloons that then pop into pink sparkles. It's very sudden and freaky, and the real Pinkie was in danger of being transformed by accident.
The slightest show of distraction from a featureless wall... and BOOM! Headshot. One right after another... until only one remains. As mentioned below a couple pinkies distract the others in ways that you would be very hard pressed to ignore.
Another clone blows into one hoof, and the other sprouts small, alien-like fingers. It'd be enough to freak Lyra out, if not thrill her to some degree.
Twilight misfiring her transmutation spell and turning a bird and a frog partly into oranges. The former was especially disquieting because when it gets hit we don't see the final product until the next scene, just a shower of feathers, making it look like it straight up exploded.
Put yourself in Pinkie's shoes for a second. There's a swarm of hedonistic maniacs on the loose... and they all look and sound exactly like you.
And there's literally no method of differentiating them from you in any way. So no matter how hard you try, you can't possibly convince your friends that you're the original.
Pinkie Pie tilting her head to the ticking of the clock while wearing a totally blank expression on her face. It's creepier than it sounds...
If somepony's duplicated by the lake, they can be sent into it. Odds are, Celestia's sealed something nasty in there.
Similar to in Magic Duel, we have something magical that can cause major problems if somepony cares to use it, with nothing keeping anypony from using it other than a bunch of thorns and somepony used it before.
Some of her facial expressions give off the same vibe. Overall, this does a good job of showing Trixie is Not Herself and is corrupted by the Alicorn Amulet.
Even before the Amulet, there's her unholy grin right before the opening theme. You don't see her eyes or her face, just her smile growing bigger and bigger...
The Alicorn Amulet in general. It has the appearance of a dark, glaring alicorn, and it corrupts Trixie into wanting to take over all of Equestria.
One has to wonder: Who is that amulet representing? Does another much eviler Alicorn exist?
The Alicorn Amulet made her go Drunk on the Dark Side. The idea something like that exists in this world is rather... terrifying to say the least and it's sold in a shady shop similar to Borgin and Burkes for anyone with money to buy...
The Cold Open, period. Even ignoring Trixie's creepy silhouette-Slasher Smile at the end, the shop is full of ominous items, including multiple bottles of green liquid with a skull-and-crossbones on the front. Poison canonically exists!
What's the first thing Trixie does upon exiling Twilight? Why, take over Ponyville and enslave its people, of course! She cuts off Ponyville's connections to the rest of the world, holds the Mayor hostage, and forces the ponies to dance for her and serve her every whim. Then she vows to overthrow Celestia and Luna themselves and take Equestria for her own. Good thing Twilight managed to get that Amulet away from her before she was too far gone... What makes this more terrifying is she very well could have succeeded. At the Canterlot Wedding was proven that Celestia can be defeated by someone with sufficient power.
Even more terrifying is that this episode confirms that any pony with the will to do so can become that powerful. Scroll back up and reread the details about King Sombra. That is what absolute power can do to a common pony; Any common pony.
Most horrifying of all? It was originally believed, before the airing of the episode, that the Amulet was a piece of Sombra, something that he himself had made. Now it has been revealed that it's just a powerful magic charm. A charm that can amplify a moderately skilled unicorn like Trixie to the 'highest level of unicorn'. Imagine if that amulet fell into the possession of Sombra, someone could stand up to Princess Celestia and Luna in a fight without it...
What was done with the amulet once they got it off of Trixie was never addressed. It could still be out there.
The age spell. Twilight's demonstration may not have been real, but Trixie's certainly was.
The fishbowl had a cloud forming inside it. Not through it, inside it. That means it was airproof. A bit longer, and suffocation could have been a problem.
When Trixie accidentally tickles Rainbow Dash, she exclaims that the spell was supposed to "make her writhe in agony". That's right, Trixie pretty much tried to use the Cruciatus Curse on Rainbow Dash.
Sleepless in Ponyville
The show had the guts to show the decapitated body of the Headless Horse in Scootaloo's nightmare.
And the nightmare about the Olden Pony, especially when she does a Jump Scare from Rainbow's bed.
"Who's got my rusty horseshoe?"
Scootaloo's bloodshot eyes after the first night. That is some painfully detailed artwork.
Luna's glowing white eyes, coupled with the split second shot of her moving through the trees.
Luna has the ability to enter your dreams. Stop and think for a moment. This means nopony really has privacy, as Luna's always watching over all of her subjects. This isn't the truly scary part: Luna is a benevolent Princess who genuinely seeks to protect her subjects from their nightmares. As scary as she is, it'd still be making her a Ron the Death Eater to see her actively abuse this power. Nightmare Moon? Not so much; remember that one of the things that drove her over the edge was ponies sleeping through her night...
Here's a more terrifying thought: Equestria is a world filled with magical threats, and creatures of magic can attack from any avenue, even through your dreams. Imagine what kind of monsters might be out there, prowling your dreams, that are so dangerous that a Physical God has to patrol your dreams every single night to ensure that they don't come after you. Now, imagine what it must have been like while Luna was sealed inside the moon for 1000 years.
The destruction of the Twinkling Balloon and seeing the Mane Cast sans Rainbow Dash screaming in terror as they plummet to their deaths.
Made worse by the fact that Rainbow Dash herself was partly responsible for making that tornado that destroyed said balloon. She may be ultra competitive, but she would never be able to live with herself if said competitiveness ended up hospitalizing or even killing her best friends. If the worst had happened, even more then blaming Lightning Dust for her indifference to reckless endangerment, she'd have blamed herself infinitely more.
This is Rarity's third time falling to her doom. She probably was having a terrible flashbacks the whole time she was falling, which would make this all the worse for her.
More Adult Fear than anything, but Lightning Dust's superficial charm (she gets along with Rainbow early on), callous disregard of others' safety (plowing past her teammates and dismissing their plight as them "needing the practice"), astonishing selfishness (getting impatient despite one of the challenges not being a race and only caring about the twister when it costs her the leadership rights), and smug lack of empathy for Rainbow's understandable anger after the twister incident seem vaguely suggestive of sociopathic behavior.
Applejack's entire family on a cart about to crash into the barn, after which the barn collapses on top of it and possibly kills off her entire family? Voilà, a family reunion to remember.
Spike At Your Service
Timberwolves are shown to be even more frightening in full CGI form. They can reassemble themselves even after being blown apart and can even assemble themselves into one gigantic being.
If you're reasonably genre savvy, you can almost see the regeneration coming because it's a kids' show and thus death on camera wouldn't normally be depicted this casually. However, now imagine you're a child. If the timber wolves really decide to come after you, even smashing them to bits won't stop them...
At one point, Discord removes his eyeballs directly from his eye sockets. The way he does it makes that moment even creepier, if for no other reason than how much of a Mind Screw it is. Discord makes a "rolling my eyes" pun and takes out his eyeballs before rolling them like a pair of dice. The eyes fall into a pair of holes in the ground and said holes turn out to be Discord's eye sockets, and the real Discord suddenly materializes on the ground and sits up. The whole scene is a moment of reality warping that would break your brain if you thought about it too much.
There is a constant sense of Paranoia Fuel surrounding Discord. We know this guy could snap at any moment. Even when he reforms, Princess Celestia still warns the girls to keep the Elements with them at all times!
Discord states that he could hear every word that Celestia said while he was in stone. So does that mean that he was sentient for the past year he was frozen, still thinking while being unable to move? What about the thousand years he was first frozen?
Due to having Fluttershy's cutie mark and destiny, Rainbow Dash is forced to care for various animals. At first, we see some funny scenes of her not being able to control the animals. Later on, the animals tie her up and put her in a pot and imply they're about to eat her.
When Twilight finishes the spell, the Elemental Harmony Regalia suddenly blast energy at Twilight, causing the others to panic and scream. There's a huge flash... and then Twilight is gone, leaving a scorch mark. Additionally creepy, in that the scorch mark is in the shape of Twilight's cutie mark.
Before she's teleported, she reacts with shock as to what's going on, then just closes her eyes and accepts it.
To make matters worse Twilight was gone for several hours from her friends perspective. It was still day when she vanished and was night by the time she came back. Her friends must have spent hours thinking that they may have just killed their friend.
It's disturbing that Twilight can accidentally switch her friends' destinies. Twilight herself definitely thinks so. It's made worse that the others don't remember their former lives, and are resigned to being terrible at what they think they must do.
Made even more disturbing since it likely means the five don't remember their families. Whether or not their relatives suffer the same memory alterations is unknown.
If Star Swirl the Bearded never finished this spell and he probably casted it several times for experimentation. Can you imagine how many ponies must have been forced to live the rest of their lives doing something they're not meant to do? What if these occurrences had a hand in shaping key events in Equestria's long history?
Two possibilities: Either only Luna and Celestia are immortal (due to them having to control the very cosmos around the planet) or that all of Twilight's friends will become Alicorns.
Or something happens to Twilight.
Pinkie's line "It's no fun being me" from What My Cutie Mark Is Telling Me is absolutely horrifying. This is Pinkie Pie, fun ponified. We've seen how fragile her sanity is before, now think what would've happened if Twilight hadn't fixed things so fast. Twilight accidentally Discorded her friends.
On that note, if the affected ponies don't remember the way things should be and everypony else is retroactively affected by the swap in friendships/family ties, what is Discord up to?
Imagine what it must've been like for the Ponies' friends and family while the cutie marks were switched. Imagine what it must've been like for the Apple Family to see Applejack's life suddenly change. Or, how about Sweetie Belle? Or, heck, even Discord since Fluttershy is the only friend he's ever had.
Princess Twilight 2-Parter
Celestia is walking through the halls of the palace when a black vine sprouts out of the ground and snakes after her. We don't see what happens, we only hear Celestia crying out in shock, then the scene cuts back to an unsuspecting Twilight (with zero indication of what happened to her).
The Everfree is even more of an Eldritch Location with the out of control vines and all.
At one point we see some vines trying to strangle background ponies like a python.
And these vines can even infect clouds, so not even the pegasi or other flying creatures are safe.
During the episode, Twilight, cut off from her friends, is ambushed by these giant black flytrap-like plants that shoot mist at her. When her friends finally arrive, she's gone unconscious, and one of the flytraps starts moving in for the kill.
According to her friends (and Discord), the first vision she saw was bad enough to force her into uncontrollable sobbing. Imagine being her friends and witnessing that.
Twilight witnessing Luna's breakdown and transformation into Nightmare Moon.
During that breakdown, Luna ends up smashing a stone arch and screaming "There can only be one princess in Equestria! And that princess will be ME!!!"
Not to mention how she laughs when she turned into Nightmare Moon.
The threatening eclipse that happens in the background.
When Nightmare Moon lands a direct magical blow on Celestia that knocks her to the ground, Celestia doesn't just go "oof", she screams in pain. You'd be forgiven for thinking it killed her, just like Twilight momentarily did. Now, consider the effect of something strong enough to knock down a Physical God hitting an ordinary pony...
That cragodile that almost chomps down Twilight is pretty threatening; it's a big scary monster that, unlike the Hydra or King Timberwolf, doesn't have any cartoony aspects to soften its scariness.
The fact that this whole mess was Discord's fault really hammers home just how powerful he is and how much damage he can do without even trying. To elaborate, before he was first turned to stone by Celestia and Luna, he planted seeds called Plunderseeds that would grow into vines that would ensnare the princessess due to lack of magic. But the magic of the Tree of Harmony kept them from growing until it began dying. In other words, even when he's not actively causing chaos, when he's not actively making trouble, even when his plans go awry, he still ends up causing chaos. All of it makes his Heel-Face Turn a lot less believable.
And then there's piece of Paranoia Fuel. Because the girls had to give up the Elements of Harmony to save the Tree of Harmony, they've lost their only means of keeping Discord in check. Yes, Fluttershy could simply threaten to not be his friend anymore, but we can't be sure how long that'll last.
When Luna raises the moon to cause a solar eclipse, the eclipse envelops her in shadow. For a moment, she has a shocked look, and gives a little cry before the shadow transforms her into Nightmare Moon.
To top things off even further, it immediately follows with Rainbow Dash and Applejack covering themselves with bees. You can only see their eyes. Thankfully, they're covered in protective suits, but we don't know that at first. One of the bees ends up flying into Gummy's nose, squirming around, and coming out the other end. Squick.
The first glimpse of the Pony Of Shadows. Supposedly, when Nightmare Moon was banished, a part of her dark power was left behind. We've already seen what Nightmare Moon can do, so imagine that power in the hooves of an immortal fragment of magic.
This episode greatly expands on the Everfree Castle, which is very... Disturbing, to say the least. It's definitely not something you would think of when you think Equestria. It's full of dark disturbing imagery, not to mention the frightening similarities to an actual real world castle.
Not to mention this all comes from the minds of Celestia and Luna, who turn out to have had some pretty dark humour in their younger years.
The fact that the Pony of Shadows is Real After All, and the Mane Six don't know that...
After Applejack and Rainbow Dash are walking through the hall with the armor... Makes you wonder how the guards looked like in the past...
Also, what's freaky, is that this is probably the first time we see the mane six with absolute fright in their eyes, especially since the animators are now working with the new animation style.
The very fact that Daring Do is Real After All creates a lot of Fridge Horror. Go back and read the entries for the "Read It and Weep" again. Now remember those are based on real events.
While Ahuizotl is too Laughably Evil to be scary, the fact that hired thugs Only in It for the Money exist in Equestria is a sobering thought. The beatdown they gave A.K. Yearling/Daring Do is pretty disturbing, and the fact you don't know she's a Badass adventurer at the time makes it scarier. (Before The Reveal, it looked like The Mafia were breaking into an innocent author's house to beat her to death)
Speaking of which, the goons that beat Daring up end up breaking her leg. It isn't mentioned, but the way you hear anaudible "snap" and she crumples to the floor immediately after leaves no doubt. She quickly splints it and from there on out, it's apparently no big deal, but keep in mind this is a fatal injury when it happens to a real horse. Even worse, they animate her with a fairly realistic limp as she walks around afterwards. Anyone familiar with four-legged animals can immediately recognize that wounded gait, it's more than a little disconcerting.
Flight to the Finish
Diamond Tiara and Silver Spoon seem to be almost sadistic here, even more so than their normal bullying selves. Their teasing of Scootaloo over her about inability to fly must have stirred up a lot of uncomfortable stuff for fans, especially for those who have handicaps themselves.
Hulked Out!Fluttershy. Especially when her voice gradually gets lower before her transformation. Be thankful she's on the heroes' side.
Mane-iac. Spike wasn't kidding when he said she went insane.
Even her very first appearance in the episode (when she climbs out of the vat) is a bit disturbing.
The Mane-iac's insane laughter when she's finally defeated. Especially how she's tangled up in her own mane like a straight jacket.
Vampire Fluttershy. The fangs, the eyes, the wings, the expressions, the hissing, the complete change in her usual demeanor to that resembling a feral beast, and even the subtly transformed cutie mark from 3 butterflies to bats, made all the creepier by the fact that she still very much resembles Fluttershy.
The creepiest part? The transformation didn't completely go away. What does this mean for our yellow friendliest friend?
The fact that the rest of the Mane Six more or less forced Fluttershy into going along with Applejack's plan is a bit unnerving.
Unintentional or not, the way Twilight said "Nopony leaves the orchard until we solve this." was pretty ominous (and Harsher in Hindsight).
Rarity having the misfortune of seeing a Vampire Fruit Bat up close and licking the apple juices off her visor. Her scream isn't much better.
The casual way Applejack treats the Vampire Fruit Bats like actual vermin. Yes, they're detrimental to apple crops, but they're shown to be perfectly sentient. Applejack just thinks they need to be exterminated, like rats.
Seeing Fluttershy cower while the rest of the Mane Six marched around her, chanting "Stop the bats! Stop the bats! Make them go and not come back!" was particularly unsettling.
The Vampire Fruit Bats themselves are pretty scary.Unlike their normal cute and cuddly counterparts,they have a more monstrous and feral appereance.The fact that they awfully resemble Stripe and the mutant bat gremlin certainly does not help matters.
Flutterbat's facial expressions.
Pinkie Apple Pie
Everything with Goldie Delicious is either this or a Crowning Moment of Funny, or a "Funny Aneurysm" Moment. Her hoarding is played in a disturbingly realistic way, and her animal abuse is likewise played as such; she's downright neglectful of her cats (not cleaning up after them, leaving one's corpse just sitting by some books), and seems to see them as no different than the items in her house, throwing them outside with junk.
"Dusty", the cat that was dead for so long it just blew into dust.
Although some people think it was actually just dust shaped like a cat, live a "dust bunny".
A "Slenderman" type character makes a very quick cameo near the end.
The Scariest Cave in Equestria. It's given a Nothing Is Scarier presentation that lets us imagine any horrific things we want that would leave the Apples so traumatized. Becomes Nightmare Retardant when Pinkie decides to take a picture (and they don't seem to suffer any ill effects afterwards, aside from trauma).
Soarin's injured wing is quite painful to look at.
Three's A Crowd
The giant worm that tried to kill Twilight and Cadance. It's design is incredibly simplistic, and somehow utterly terrifying at the same time, especially the mouth. Worse, we get absolutely no warning that it's coming.
It's made even creepier when you realize that DISCORD didn't know what it was!
And it manages to actually get him sick. While it is funny to see him getting his just deserts, it's not as funny when you start asking yourself what kind of creature could do that to a Reality WarperMad God?
Early on, Discord sneezes on Applejack and Rarity, turning them blue like him. Even though it's revealed that he was never sick, and that the two are shown back to their normal colors, what if the "blue flu" was real? What would have happened to the two?
Pinkie really comes off as creepy this episode what with her trying to "help" Fluttershy with her advice and compliments while also getting in her face about it. Plus her "peek a boo" scene in Big Mac flashback. And a particularly jarring scene in Fluttershy's cottage where there's a closeup of her climbing the ladder while trying to comfort Fluttershy in her usual way.
It Ain't Easy Being Breezies
Seabreeze's attempt to get home on his own, making clear why them staying in Ponyville is a very bad idea.
Seabreeze's urgency to get home is in itself a good dose of Adult Fear, since he has family waiting for him and the others don't even seem to see the dire-ness of the situation they're in.