This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Ever After High
The Evil Queen. She lives up to her reputation and then some.
The plague that caused Wonderland to be quarantined off comes to mind.
The premise of the series is that the fairy tale characters' children are forced into their parents' roles, even if they don't want them or have befriended someone on the opposite side.
In the webisode "Stark Raven Mad", a teacher asks Lizzie Hearts what she thinks they should do with Raven. Lizzie's response?
Lizzie: Off with her head! (punctuated by her slicing the head off of a playing card)
Although later we find out this is a Wonderland quirk of hers and she doesn't actually mean that she wants people's heads cut off every time she says it.
The fakeBad Future Raven sees in the Wishing Well in Thronecoming.
While everyone looks like they have gone through Hell, we see Ashlynn is clutching Hunter's keychain, indicating that something really bad happened to him.
Briar's destiny as shown in Thronecoming, visualized by vines with pretty little pink roses wrapping around Apple's body, covering the room and guarded by some sort of tree monster. Worst of all is how quickly it happens - Apple accidentally touches the spindle, goes limp and they come in through the window. Her hand is raised, finger is still bloody. Hats off to the animators making what should be a pretty peaceful fate look so unnerving.
Evil!Apple in Spring Unsprung goes from cheating in a cooking contest to sucking the life and wonder out of Ever After, and if not for Ginger, she would have succeeded too. She also didn't give a hoot that she was going to be affected as well.
At the end of Way Too Wonderland, the Evil Queen hints that Raven signing the Storybook of Legends and inheriting her powers are parts of her plan to escape.
The briar thorn walls could have very well doomed Apple and Raven to a sharp, pointy, and painfully slow death by bleeding out if Hunter hadn't been around to save them.
Bella sister's fake corpse. Found in a dank cave with the abandoned, rotting remains of an awful, solitary life, with "I SHOULD HAVE SIGNED THE BOOK!" signed above her in bright red paint.
The Puppy Potion. Imagine being in Raven's shoes, innocently pouring a mixture onto your pet puppy to watch it turn into a horrible bone rat.
Why does Apple want to stick to the story so much? It doesn't involve accidentally falling into a well, and drowning to death. Sure, she was only there for 2 minutes but still.
Raven's nightmare about what would happen to the Snow White story and its characters if she refused to sign. Apple's head in a goblin bowl shouting "Boo" is particularly chilling—more so because it's the last image before her Catapult Nightmare.
Raven Queen's taste of power during Legacy Day. It's frightening how close she came to becoming her mother. What if Dexter and Maddie hadn't said hello?
The Unfairest of Them All
Raven is almost killed by an angry mob.
Hood Hollow in general seems to be a pretty nasty place—in addition to the attack on Raven, the townsfolk are viciously prejudiced against Cerise when they find out her parentage, calling her an abomination and threatening to banish her.
Maddie almost gets unjustly expelled for what basically amounts to a Crime Against Humanity.
The climax: the Evil Queen came this close to freedom.
The jabberwocky is free. And it's just going to take a nap before it starts to wreak havoc...
Hell, its description in general. It'll wait a few years to regain its strength before it terrorizes all of Ever After...
It waits, but only a few months tops.
It's a Wonderlandiful World
The jabberwocky. It turns Ever After High into a twisted copy of Wonderland, transforming most of the students into objects and animals while it's at it. It gains power by absorbing Wonder from Wonderland residents, as it does from Maddie's dad in the climax. And if it can't absorb anything, it just eats people.
The twisted Ever After High. Living furniture that runs rampant, halls and doorways less whimsical more nightmarishly labyrinthine, the constant threat of the Jabberwocky...
Next Top Villain
Sparrow Hood coming very close to killing Lizzie Hearts by scaring her horse so badly it got spooked by the troll at the bridge and ejected Lizzie into a ravine (with an entire crowd of students and faculty watching, no less), just to get the prize in Mr. Badwolf's treasure vault. It's a good thing Duchess transformed when she did, otherwise...