For example, I will definitely include:
Hunchback of Notre-Dame
Prince of Egypt
Pinocchio

Snow White and the Seven Dwarfs.

9
Watership Down
The Secret of NIMH
The Black Cauldron

Thank you! I would also like to add Spirited Away, I forgot about the other types of animation.

My Little Pony: The Movie.
The 1986 one. (link) I'm serious, this movie was so dark and depressing I can't sit through it.

Basil: The Great Mouse Detective
Kung Fu Panda 2
Laputa: Castle In the Sky
The Lion King

Theres also Pom Poko...and Felidae, Akira, Grave of the Fireflies, Wizards, Fire and Ice, The Plague Dogs, Heavy Metal, Heavy Metal 2000, Fantastic Planet....

The Nightmare Before Christmas
James and the Giant Peach
Corpse Bride
An American Tail
Anastasia
The Land Before Time
The Princess and the Frog
Coralline
Frankenweenie
Paranorman
Little Nemo: Adventures in Slumberland

Here are some of the movies that I think are dark:

The hunchback of Notre Dame
Prince of Egypt
Pinocchio
Grave of the fireflies
The black cauldron

The Miyazaki movies were also dark in my opinion.

The Last Unicorn
Little Nemo: Adventures in Slumberland