For me:
The Black Cauldron.
Filmation's Pinocchio and the Emperor of the Night. (It stars James Earl Jones and it's quite dark beyond belief that it has to be seen on youtube even for part 5 of the movie on there which is a disturbing scene)
The Secret of NIMH.
Watership Down.
The Brave Little Toaster.
Fire and Ice.
Wizards.
"You gotta be Fking kidding"-The Thing.
The Secret Of NIMH
The Hunchback Of Notre Dame
Watership Down
All Dogs Go To Heaven
The Black Cauldron
Spirited Away
Plague Dogs
Felidae
Heavy Metal
The Brave Little Toaster(first one)
Not a movie but The Moomins cartoon series entitled "Moomin" (1990) is really dark and grim in places for a kids animated series. I would recommend it as its now available on DVD.
And I mean the cartoon series not the puppet one. Link to here
http://www.imdb.com/title/tt0247117/
They think we're the demons now - Prue Halliwell ~ All Hell Breaks Loose ~ Charmed
Coraline
Tim Burton's Corpse Bride
The Nightmare Before Christmas
Snoopy Come Home, because we don't know how serious of an illness the little girl in the hospital has.
shareThe Simpsons' "Treehouse of Horror" episodes!
Opportunity is missed by most people because it is dressed in overalls and looks like work. -Edison
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Mary and Max.
shareRankin Bass' the Hobbit and Return of the King, same animation as TLU.
Watership Down
The Fantastic Adventures of Unico
Unico and the Island of Magic
The Sea Prince and the Fire Child
Flight of Dragons
The Secret of NIMH
The Land Before Time (NOT ANY OF THE SEQUELS!)
All Dogs Go to Heaven
Pretty much anything by Don Bluth.
Pinocchio and the Emperor of the Night
The animated/Rotoscoped Lord of the Rings
The Nutcracker Prince
Nutcracker Fantasy (more stop motion but hell it was creeeeepy)
"Slice, Pull, Staple, its a boy!" - Maul57
I can handle the whatever!
Not sure if any one has seen the Magic Pony. Its a Russian film from the 70's. This along with the Last Unicorn, and Flight of Dragons were some of my favorites as a kid. Here's a link:
https://www.youtube.com/watch?v=f0m-0bvap5A
Titan A.E.
Bless Don Bluth.