Original Diesel 10 from the Thomas and the Magic Railroad. Wanted to take over the island of Sodor, destroy Lady the magical engine, and scrap all the steam engines. For context, in the Thomas & Friends world, being scrapped is the equivalent of being burned alive and dismembered.

The Beast from Over The Garden Wall

Just everything about The Clone Wars. It's basically Baby's First 'Nam. Seven seasons of carnage as millions of sentients (and millions more arguably sentient droids) get sent into a meat grinder so that Palpatine can consolidate power. And it works.

To this day, I'm stunned that something so dark and cynical ended up being a hit "children's" show.

The Lich

Zaheer from Legend of Korra. Using air bending to suffocate the earth queen was hella graphic.

Joker in Batman the animated series. Motherf***er was crazy

Plankton from SpongeBob

"F is for fire that burns down the whole town. U is for uranium bombs. N is for no survivors when you..."

Him from Powerpuff Girls

Venjix was the main villain in Power Rangers RPM. That season is, by a landslide, the darkest Power Rangers season.

His armies killed off nearly all of humanity. He performed human experimentation to turn humans into cyborgs (along with things like memory wipes). He was created (for context, he is a computer virus) by a teenager who was kidnapped and taken into a sort of experimental think tank where she lost her childhood, basically her humanity, and even her name (in that regard one could argue that the two faceless nameless agents that kidnapped her are also villains in the show despite only appearing in one or two episodes).

That shit's dark.

Cell from Dragon Ball Z. Even in the edited dub, they showed him drinking a man alive.

The Child Catcher from Chitty Chitty Bang Bang...Need I say more?

GOLB from Adventure Time.

Dudes the anti-life equation given "form"

I’m surprised no one has mentioned Fire Lord Ozai.

He’s dark in a lot of ways but his relationship to Zuko is especially mature for a “kids” show.

Syndrome from The Incredibles. It always felt a bit higher-stakes to me as a kid even when I didn’t fully comprehend what was going on, but when it clicked that he MURDERED so many superheroes just to get back at Mr. Incredible..? holy shit!

Other Mother from Coraline those eyes, those button eyes.

Didn't Gargamel on the Smurfs basically just want to cook and eat them?

Bill Cypher was absolutely terrifying. But hey, at least he's dead.

...he's dead, right?

Mrs. Trunchbull in Matilda. A movie not a series but still. She killed Miss Honeys' father to steal his mansion, tortured this woman including several little children who she threw inside a sharp nail ridden cupboard. She was so scary.

The D-Reaper from Digimon Tamers.

Tortures and gaslights a grieving child for days on end in order to use her trauma as fuel. Has zero concept of morality or why what it's doing is wrong, because it's only doing what it was programmed to do: Delete things that have "exceeded their intended parameters". Which it decided now means "all of humanity".

Slade (Deathstroke) from Teen Titans. I went back and watched the episodes where Robin was his "apprentice" and then "Haunted" (where Robin keeps seeing Slade) gave me the creeps.

Hexxus from Ferngully: The Last Rainforest

The Poacher from The Rescuers Down Under

Frollo from The Hunchback of Notredame.

Man literally allowed his boner for a 16 year old gipsy girl to burn down a sizeable part of Paris. There was no grand plan of terror and evil: it was literally an extremely creepy horny maniac with too much power on his hands.

For anyone old enough - the Care Bears 2 movie. I do not remember much other than the lion carebear. And the blond kid who was absolute pure evil

Yakone in Legend of Korra is a fucked up monster who even ruined the lives of his kids and made them villains.