This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Once Upon a Time in Wonderland
Episode 1 - Down the Rabbit Hole
The Cheshire Cat. It's far from the goofy creature you remember from your childhood. It has horrific red eyes, a row of monstrous teeth that's in a perpetual Slasher Smile, and it's hell bent on eating Alice. Also, it has the creepy, pitched-up voice of Keith David.
They were about to lobotomize Alice without anesthesia!
Episode 2 - Trust Me
Jafar casually disintegrating a room full of frozen people, just so the Red Queen won't have any excuse to put off helping him. He also completely paralyzes her except for her eyes, just for mouthing off at him.
The entire episode opens up with him murdering someone. Slowly and painfully, at that.
Just about every scene between Jafar and the Red Queen makes you feel terrified for the latter's safety given how Jafar is not at all subtle about how threatening he is. It almost calls to mind an abusive relationship at points. Until the end when the Red Queen gets leverage over him and demands he stop treating her like crap. You Go, Girl!.
Episode 3 - Forget Me Not
The Caterpillar keeps screaming severed heads as trophies.
So much of what Jafar does in this episode, particularly force-choking the Knave and then proceeding to levitate Alice into the air and torture her by having her limb muscles stretch out farther and farther.
Akil's death, which sets Jafar truly on his path to becoming the manipulative puppetmaster we know and cower in fear of. It's made all the worse by the fact that Jafar is obviously affected by the death of someone he seems to know and like quite well, but still lets the man die for the sake of learning one spell that isn't even tangentially connected to Jafar's revenge.
To save Knave's life, Alice wishes that if he dies, she dies. This essentially ties them together as it means that she's in trouble if ANYTHING threatens him, not just Jafar (and there are implied to be a lot of people after his head).
Jafar interrogates the White Rabbit and then, out of freaking nowhere, cuts his foot off.
Episode 6 - Who's Alice?
The Boro Grove: It intoxicates you with a pleasant scent that makes you feel happy and forget everything that bothers you. Sounds nice, right? It also makes you want to stay there forever and eventually you turn into a tree and are stuck for the rest of eternity.
Episode 7 - Bad Blood
The scene where the Sultan holds young Jafar's head underwater and tries to drowns him. If there are children watching this show, they're certainly traumatized now.
Jafar's "Well Done, Son!" Guy breakdown when he first confronts his father as an adult. It's partially tragic and partially terrifying, as he comes off as completely psychotic as he begs his father to call him "son".
Episode 9 - Nothing To Fear
The Jabberwocky. Everyone in Wonderland is afraid of it and advise Jafar against releasing it and by the end of his encounter with her, during which he encounters the ashen-white corpses of her previous victims, she taunts him with almost a bored tone, and she effortlessly makes him physically re-experience his near-drowning without touching him, he seems to agree.
The Jabberwocky's cavalier attitude towards the fact that she's pinned to the ceiling with a sword right through her. She seems to see being imprisoned and impaled for a hundred years as more of an inconvenience than a defeat. Also, "I'm not worried about getting inside your head. I'm already there."
Episode 10 - Dirty Little Secrets
As if Lizard's seemingly senseless death wasn't bad enough, this episode gave her a significantly worse fate: having her two eyes pulled out of her skull just for Jafar to view her last glimpses.
Nyx, the Guardian of the Well of Wishes. Apparently one of the writers thought the series was lacking a Stringy-Haired Ghost Girl.
You think the Jabberwocky preying on fear just for kicks was bad? Try seeing her do the same thing, this time with an actual intent. Poor, poor Anastasia never stood a chance.