Anything involving Joker, particularly the following quote, which is positively chilling...
Joker:We couldn't [adopt] legally, but then we remembered you always had a few spare kids hanging around... so we borrowed one...
The way Batman just growls "I'll break you in two".
The soundtrack "Joker Family Portrait" makes it all the worse — while it starts off as a light and bouncy (if somewhat morbid) riff on 50's sitcom themes, complete with Mickey Mousing, everything stops dead with a sudden low piano chord as Tim is revealed strapped to the operating table. As both he and Joker begin to laugh uncontrollably, the horns play a Dark Reprise of the earlier "family" leitmotif. Worst of all is the high, screaming electric guitar notes, apparently created with the vibrations from a music box.
A line you'd never want to hear the Joker say:
Joker:In time, he told me everything... Bruce.
When Terry heads back to the Batcave after being assaulted in the nightclub, he finds the clock smashed, "HAHA"s spray-painted all over the cave (and it's worse in the uncut version of the film; the paint is blood red) and worst of all, finding Bruce on the floor by the computer apparently dead from Joker venom.
One could argue the uncut version is darker, but Bonk's death in the re-edit version has him hit with Joker gas, dying of laughter as slowly as possible with his teammates looking on in fear.
Even more chilling is the Joker's death scene, which varies depending on which version you watch.
In the edited version, the Joker gives Tim the laughing gas gun and tells him to "make [Batman] one of us". However, Batman's voice easily breaks through Tim's mind, and he puts away the gun and pushes the Joker into a room with two tanks of water; the Clown Prince of Crime gets knocked into one, gets soaking wet, and tries going after Tim, but he slips and turns on the electrode machine. The scene immediately cuts to the outside of the room, where his horrifying death scream is heard! Nothing says it's Nightmare Fuel for kids like this one! And you thought the film developers were trying to make things any easier. It doesn't.
The uncut version is even more terrifying: the Joker tosses the "Bang!" Flag Spear Gun to Tim, then pulls Batman high as his trophy and says, "Make Daddy proud: deliver the punch line." Besides his chilling voice, Tim giggles like a maniac and, if you've seen the scene with Bonk, you know what's gonna happen: he pulls the trigger once and the "Bang!" flag pops up. When Batman tries to calm him down with "Tim...", he keeps giggling and doesn't calm down very easily, only more slowly than the edited version. Also, the aforementioned blood on both Batman's and the Joker's mouths and the same creepy music don't help matters either. The Nightmare Fuel starts getting higher and higher as the Joker, the blood still on his mouth, loudly barks out, "DO IT!!!" And the creepy music starts escalating Up to Eleven as Tim laughs more loudly and is about to pull the trigger as if this were the end of Batman. But once the boy finally fires the gun... the projectile doesn't hit Batman at all. Instead, it hits the Joker in his vital spot, sending him flying across the room onto the giant building blocks. Gasping weakly, he mutters out his ironicFamous Last Words: "That's not funny... that's not..." The Nightmare Fuel finishes off with his dying gargle as he gets choked up in blood, and then his body falling lifelessly onto the floor. Truly a Family-Unfriendly Death that's less scary than the edited version, but still...
The background music that accompanies this terrifying flashback scene, "Arkham Mayhem", is almost all Nightmare Fuel and part Tear Jerker. Give it a listen... if you dare!
Joker's Villainous Breakdown near the end. Imagine, if you will, as Joker's usual demeanor is chipped away piece by piece as Terry openly mocks him to try and catch him off guard. First he gets snappy, which isn't so bad. Then he screams "YOU'RE NOT BATMAN!", and completely loses it, and manage to swing a table at Terry... A little surprising. Pins Terry down with the table, stands on top of it, yanks the mask off and proceeds to strangle Terry, producing one of his most insane laughs ever given, sounding more and more unhinged as he speaks? Downright scary, especially when you get a POV shot from Terry's eyes for a few seconds.
Joker (Looking furious and euphoric): C'mon, McGinnis... You miserable little punk! LAUGH! IIIIII CAAAAAAN'T HEEEEAAAAAR YOOOOU!
Before that, Tim knocks off the beakers before making his hideous transformation worthy of Dr. Jekyll and Mr. Hyde into the Joker via microchip. And Tim's voice evolves into that of the Clown Prince of Crime, which makes it all the scarier.
The fact that despite voicing the character for nearly a decade by this point, Mark Hamill actually felt uncomfortable voicing him in this one. Let's put that in perspective. In the original series, the Joker repeatedly killed people in droves, abused his girlfriend, stalked a guy for years on end, and created Joker venom, which is basically Nightmare Fuel in gas form. All of which was turned Up to Eleven in Batman: Mask of the Phantasm. And yet what the Joker did in this movie unnerved him.
The Grand Theft Me trope is quite chilling in virtually any work of fiction, and here is certainly no exception. The Joker states that with time he will learn to permanently suppress Tim's natural consciousness, effectively causing a Death of Personality. Also, as he's using Tim's body, he can impersonate Tim's voice and effectively deceive people—including Tim's own wife—through phone calls.