Alternative Character Interpretation: Did Batman really think Scarecrow was behind the events of the comic, or did he just tell Dr. Arkham that for the staff's own peace of mind? (It's not like Batman hasn't had his fare share of supernatural experiences) Or was he even suggesting it as a cover story?
Anytime we see anything from Doodlebug's point-of-view
Anytime Death Rattle shows up. All he has to do is sit there and you're terrified. In terms of scariness, he could definitely give Hannibal Lecter a run for his money.
Warren White's metamorphosis throughout the whole story is this. Especially after being locked up in Mr. Freeze's ice cold cell which lead to his iconic disfigurement.
Humpty, he is genuinely insane and dangerous and he does not seem to understand it. When he says that he wants to fix Warren after explaining what he did to his grandmother he is horrified.
Everything about Jane Doe. A hollow person who studies someone only to kill them and take their place, then she'll get bored with their problems and will try finding someone else to impersonate. When she performs a three steps Borrowed Biometric Bypass, she turns out to have kept the eyes, hand and an audio recording of Dr.Carver begging for her life.
The demon forms the supervillains take when they're unleashed against Aaron Cash.
Killer Croc, both before and after demonic possession. Which makes Aaron Cash beating him even more awesome.
Squick: Among other things, there's what Jason Blood keeps around when Bullock visits him and all the stuff in Nightmare Fuel.
Humpty Dumpty's back story. A kind, gentle guy whose life was a series of bad luck since childhood. As a child, his house was demolished by accident, dog ran over by an ice cream truck, and parents crushed by their Christmas tree. Then he was taken in by his physically abusive grandmother, who beat him and forced him to repair shoes for her. But he remains a kind, gentle guy, and all his crimes are merely him trying to fix problems in the world, even the murder and stitching of his grandmother.