This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Keys to the Kingdom
The Skinless Boy.
The worms under the Incomparable Gardens are pretty bad.
The two clockwork figurines that rip out their prisoner's eyes. And they have no qualm about going out and getting a different pair if they can't find the one they want. It used to be vultures that went for the liver.
The Architect. That's right everyone, your god's master plan is to kill you all, and the only things preventing her from doing it are a bunch of selfish, immoral jerkasses who don't care that you exist.
Most Nithlings are quite horrifying in their own right, but special mention goes to that bizarre cricket thing in Grim Tuesday as well as the massive hordes Leaf has to fight off as the temporary Lieutenant Keeper.
Drowned Wednesday's first meeting with Arthur. The entire affair is just so gruesomely described for a children's book that it adds an extra layer of disgust to the sheer horror of the basic imagery.