The scene from Labyrinth when the Jennifer Connelly is looking for her brother in the house is kind of scary for kids.
Oh, and the banshee scared the hell out of me when I was a kid.
The “pink elephants” scene in Dumbo always kind of freaked me out as a kid. It still kinda gives me the willies.
Raiders of the Lost Ark was a kids movie, right? It was rated PG! #meltingnazis
Winnie the Pooh and the Blustery Day - Heffalumps and Woozles
As a kid I was home sick from school one day and I was watching a movie called A Mouse and His Child. The main characters were toys and in the movie a rat pulls apart a toy donkey with a wrench. I turned the movie off immediately and never forgot that scene, it freaked me out so much.
First thing that I thought of!
I haven’t actually seen the movie, but I have it on good authority that there are a couple of really creepy scenes in The Brave Little Toaster. One involves a junkyard and the other has visions of Hell or devils and fire. I saw them both on YouTube two or three years ago. Can’t look them up now, but I expect they’re still there.
Missed the edit window. It wasn’t demons–it was a clown from hell.
And let’s not forget the “Hellfire” scene from Hunchback of Notre Dame. I love the scene and the song, but it’s pretty creepy and heavy for the kiddies.
Also, “Night on Bald Mountain” from Fantasia.
I know the scene. Amazing animation!
Not a kids’ movie, but related. The Mad Hatter and March Hare’s tea party as created by Jim Henson’s Creature Shop for the movie Dreamchild have never been more disturbing.
Thirding Coraline. It is perhaps the only horror movie that I like in the classic way. Meaning that you want to be scared on purpose and let yourself be scared. The reason that it can scare me a bit is because it uses the same animation technique as a lot of the classic holiday specials that I was exposed to as a kid, which were scary themselves as a kid and so it reminds me of watching them. If I hadn’t been exposed to them I would have found it merely droll if somewhat creepy in a Burtonesque way.
It may also have scared the kids watching it in the same way a little. When I saw it in the movie theatre, I sat in the front row and upon standing up and turning around at the end all the kids were quietly gripping their seats. Which could have been a sign of rapt interest or extreme boredom 
Almost half a decade later, I can still remember details of the nightmares about Maleficent I had after seeing Disney’s “Sleeping Beauty.”
Dumbo the Elephant was a disaster, stolen from Mom and taunted by crows. No one ever buys it even if free at the annual garage sale.
In the witches laboratory in Snow White. There’s a sort of dungeon, with a door that opens into the floor of the room. Inside is a skeleton, and his arm is reaching out toward a water pitcher, just out of reach. As the witch leaves the room she kicks it toward the bones yealling “Have a drink!!” in a nasty voice.
Never saw Darby O’Gill, but as for the others, boy howdy, I’m with you there! All of them creeped me out/scared me as a kid.
Dot and the Kangaroo - The Bunyip
Toy Story - when Buzz and Woody are in the neighbor’s room with all the mangled toys.
Yeeeah 
The rest of the movie’s not any better. That damn thing scarred me for life. A couple of years ago I tracked down the video and watched it again. I can say it’s just as creepy watching it as an adult as a child. For some reason, the scene with the infinite can of dog food always creeped me out as well.
The Secret of NIMH also creeped me out as a kid.
Please don’t YouTube scenes of The Brave Little Toaster…get the dvd somehow and watch the whole thing! It’s fantastic. And yes, there are a few creepy scenes.
You know, I only got this movie when I re-viewed it as an adult. As a kid I just thought it was a cartoon about mice, but as an adult I actually understood what was happening, and what was going to happen to them.