That was my pick. I hadn’t seen it as a child but we got it for my 18 month old daughter a while ago. She loves it, although she probably doesn’t understand anything yet. I remember thinking it was a hell of scary scene for a kids movie.
There were definitely a few things in the Goonies that were scary.
Also, I was an adult when I saw it but how about when that dog hangs from the bridge in “Babe: Pig in the City”. That was some messed up shit.
Oh, yeah, the Secret of NIMH - I had almost forgotten that shudder
Little 4-year-old me, for the first time in the cinema, was also really frightened by Disney’s The Rescuers. Especially the scene near the end, when they are in the cave, trying to get the diamond, and the flood threatens to come back in - I was terrified at the thought of being drowned in a cave (and still am).
ETA: Later, I read the book it was based on, which was even more terrifying - the mice did not have to rescue a cute little girl, but a Norwegian poet, half-starved, locked in the prison cell of an Alcatraz-like fortress, guarded by a sadistic guard who kept butterflies mounted on pins. Yikes!
Seems Disney is a running theme in this thread.
I’ll never forget taking my 4 year old to see Finding Nemo. In the first five minutes, Mom and all but one of her babies become lunch to other sea creature. We had to leave the theatre my daughter was sobbing so hard.
The scenes in E.T. just before the space suit guys arrive freaked me the most…where both Elliot and E.T. are deathly pale and sick. Ick.
Raiders of the Lost Ark wasn’t exactly a kids movie, but probably was the scariest movie I saw as a kid…the melting Nazis and the avenging Ark Angel were way too much for me.
Those damned flying monkeys. Never have gotten over them. My kids were so freaked by them (on video, no less–I was traumatized at a Saturday matinee. 75 cents to ruin your life!), that they have never watched the whole thing.
The abominable snowman was fairly nasty. Somehow I always liked the Grinch, though (until Jim Carrey ruined him).
Charlie and the Choc Factory–I remember the boat trip well, but cannot recall anything but fast motion, colored lights and Wonka being strange (he was kinda freaky throughout)–did I miss some images? I think I am glad I did. Johnny Depp’s take on Michael Jackson was also disturbing.
Tribbles freaked me out–that they could be growing and multiplying in small enclosed spaces made me shudder. Gremlins was NOT amusing to me…
There was a Henson movie with some Muppets, but mostly about a smallish girl and boy (who were a type of something, halflings or something)–it involved white and black magic or some such–there was some kind of tribunal that was very scarey to me.
Chitty Chitty Bang Bang had very scarey parts, as did Tom Thumb-one guy beating the shit out of another on a stone floor, IMS-- and Oliver (the musical, not the animated one).
Hunchback (disney version) was sick and twisted to me, an adult–but I could see a child being frightened. Mulan had some intense bits, as did Lil Mermaid (that octapus was scarey!).
And of course, let us not overlook, Cruella DeVille (animated).
The Dark Crystal. The Skekses (big vulture-like creatures) are probably what you’re thinking of as far as a scary tribunal in that. Nasty things.
I came in here specifically to mention All Dogs Go To Heaven and find I got scooped by the OP. 
There was a scene in Hell, IIRC, that I had to go stand outside the theater for because I just wouldn’t sit through it.
I’m always the only one who mentions it, but I found The Devil and Daniel Mouse extremely traumatic. Heck, I still do! I’d love to know if anyone else remembers it.
Thanks, Bayle.
Now, if only I could actually remember* Escape to Witch Mountain* or No Deposit, No Return, there are probably scarey things in those as well…
Watcher in the Woods scared the Holy Creeping Jesus out of me when I was little, to the point where I became obsessed with it and it became one of my favourite movies, tho it still terrified me up through high school. I haven’t watched it in a long time, it probably still would! All the ghostie POV shots, through the woods…Karen’s face showing up in mirrors and windows…that terrifying little girl writing backwards and speaking all deep and slowly: “Nearly too late…hardly ever happens…”. GAH!
I just scared myself even thinking about it.
And add me to the list of people who were frightened by the movie E.T., although I was scared to death of E.T. himself more than the hazmat guys. When he was laying on the floor all white and disgusting, and croaking “MOOOOOOMMMMMM”, I would start shrieking and my parents would have to remove me from the theater. Three times they tried to take me to watch it, I’d promise I’d be fine, and then that part would come and I’d lose it. I never actually saw the movie all the way through until I was about 15.
Anyone else remember Dot and the Kangaroo? I loved this movie, but the Bunyip scene scared the shit out of me as a little kid. (And the end of the movie, when the kangaroo changes back into live-action and Dot is yelling “come back! come back!” made me bawl for hours, according to my parents, who still think this is funny, twenty four years later.) The bit where they get chased by dingoes wasn’t my favorite either.
My other traumatic moments have already been mentioned: Augustus Gloop getting stuck in the tube (oddly, the psychadelic boat ride did nothing for me), Lampwick and Pinnochio turning into donkeys, the trees throwing apples at Dorothy.
Another vote for The Dark Crystal, and I was an adult when I saw it. The Skeksies were way too powerful, and the halflings survival was miraculous.
You guys already covered E.T. and Darby O’Gill and the Little People. So I will just add Rikki-Tikki-Tavi. I am terrified of snakes to this day and even if Rikki didn’t cause it, it sure didn’t help any. 
Trek isn’t really kiddie-fodder though, I mean, things like the Salt Vampire in The Man Trap were a little jarring, but it was targeted at adults.
I guess I was an unusual kid in that I mostly liked the scary stuff, but what really scarred me was when people were mean.
I tell you, I will never forget when Willy Wonka YELLED at Charlie and his grandpa when Charlie came to claim his prize. That whole office atmosphere, the ticking clock, the serious expression, his face reddening and his hair flying about, “I said GOOD DAY!” …oh, I cried. And since then I have never wanted to watch that movie again.
Of course, there were a few scary images that actually did scare me… the flying monkeys in Wizard of Oz absolutely did, but really not nearly as much as the mean lady who played the Wicked Witch. The Witch herself didn’t scare me NEARLY as much as the lady-on-the-bike she was based on.
Also, a hearty second to whoever said The Peanut Butter Solution. I was terrified.
I agree; that was just heartbreaking.
6 pm broadcast 5 days a week
on a channel that had an afternoon kids line up
The wolves in Narnia were pretty scary, too.
My sister totally freaked out at the scene in The Black Stallion, when the violent horse is caged on the boat and lashes out at anyone who gets near.