pretty much all your suggestions I remember, especially courage. that show was like an animated version of That's So Weird (the weird stuff at least). Anyway, for rugrats, I remember the episode when angelica heard that her parents wanted another baby, and she got all anxious and worried over what the baby will be like. basically her vision of her new brother was very scary, not only in its voice (which sounded like an adult), but in the way it acted. it was a jerk and iirc tried to lock up angelica indefinitely in a closet. and it also ate her. there's some more unsettling stuff about that baby brother but i can't remember. tough it looked like a baby, it certainly wasn't.
another rugrats moment was at the end of an episode where chaz, i think, came down to Stu's kitchen to see what he was doing, then Stu had this high clown voice and he turned around to reveal a clownish face (w/o makeup of course) and the episode ended with Chaz screaming, I think the episode was about chucky overcoming his fear of clowns.
The Elephant Parade from Dumbo was another one, though my brother was the one who was afraid of it many years ago.
another nightmarish thing was not from a cartoon, but i think is worth mentioning. It was the short purple monster in Ghostwriter. I'm too afraid to even look for a picture of it online to post so my words will have to do. In fact, I'm so terrified of it I probably won't read what anyone else has to say because they might post a picture of it. There'll probably be people who think it looks funny, rather than scary, but at the time i first saw and heard this monster i was around 6-8 years old, it's been well over a decade since i've seen it and the image is still haunting. from what i can remember, this thing was basically slimy, melting, dripping. It wore a black jacket with pants and shoes. It was perhaps 2 feet tall and had a hideous grin and i think crooked eyes.I believe it was a doll similar to Chucky, but how it came to life (if it wasn't alive already) i don't know. (Or even if it was a doll at all) I can't remember if the monster wanted to kill the main characters, but i wouldn't be surprised if it did. I don't know what it was trying to accomplish in the first place. Nevertheless, it is a creepy, evil thing.