The last part of the original Joker's death scene in the uncut version. Not because of who died, but because of how the events that led up to it completely destroyed the Bat Family. Especially when the de-brainwashed Tim starts laughing madly after the Joker's death... then he starts crying and whimpering, and poor Batgirl can only hug him.
YMMV, but Joker's last words in the uncut version:
Joker: That's not funny... That's not... [chokes on his blood as he falls to the ground, the flag impaled in his chest]
Batgirl's reaction, and her attempt to comfort Tim.
Batgirl: It's okay, Tim. It's okay.
And to drive home the Tear Jerker in this scene, imagine what's going through Bruce's head at that moment. Over the course of Batman: The Animated Series, Bruce's sense of empathy has become impaired by his personal scars and years of battling personal tragedy after personal tragedy. By this point in his career, it's doubtful that he can feel much emotion at all without being driven to his breaking point. Now which is the greater Tear Jerker in this scenario: Joker mind-raping poor Robin through sheer torture, or Batman knowing he SHOULD feel something, but feeling nothing, and spending the rest of his life feeling even MORE helpless to save the people he cares about?
In a Freeze-Frame Bonus, Batman's reaction to Joker showing him Tim's torture is horror and sadness. Before that, he does the same reaction once he sees the fully transformed Tim.
Batman might have felt Unstoppable Rage during that scene, considering he throws a knife at Joker's head which Joker barely dodges and threatens to break Joker in two.
And it's not just young Tim in the flashback who's messed up by what happened. Consider how adult Tim feels just before going under, at the end:
Tim: Fun and games. Boy Wonder playing the hero. Fighting the bad guys, and no one ever gets... Oh, God. I killed him. I didn't mean to.
Although it's not stated, it can be implied that this event was what motivated Batman to cut ties to not only his sidekicks but to the Justice League as well, includingWonder Woman.
While some consider Harley Quinn going along with Joker's experiments on Tim her crossing the Moral Event Horizon, think for a moment. This woman started out as a psychologist and, despite her being drawn to Arkham for the thrill of the more "extreme personalities," she couldn't have entered the field without some kind of desire to help people. And now, she is Joker's accomplice as he tortures and mind-rapes Tim into "Little J." It's yet another painful note on their twisted and sad relationship, and another display of how Joker destroys anything that he touches.
Going off of that and taking it even worse, she casually tells Batgirl that she'll "make it right", in regards to Robin being tortured and completely screwed-up. She herself was twisted to think that she could take a kid that underwent horrific Mind Rape and somehow salvage at least a reasonably well-adjusted, functioning adolescent out of that emotional wreckage?
The other thing is that, for the warped Harley, what was done gave her what she's wanted for a long time. A chance to settle down as a family with her Puddin', no more fighting, just a happy family. It's the end of the battle with Batman, and she's getting a happy ending.
The fact that the Joker dies for good. As utterly twisted as their relationship may be, by this point, they've been together for years. Harley has watched him cheat death before on multiple occasions, and been distraught, only to have him pull through. But not this time. This time, she's going to be hit with the realization that her Puddin' isn't coming back.
Watching Dana get hurt when the Jokerz attack her and Terry at the nightclub. Poor girl is nearly killed and has absolutely no idea why.
Bruce:[looks at the cases holding the Bat Family's suits] I had no right to force this life on you or anyone else.
Terry: Hey, I was the one who broke in and swiped the suit, remember? Yes, there was my dad's murder, but we come from two different worlds, Mr. Wayne. I wasn't like you or the kids you took in. I was a pretty bad kid once. Ran with a rough crowd, broke a lot of laws, to say nothing of my folks' hearts. The kind of punk you wouldn't have wasted a second punch on back in the day.
Bruce: Your point?
Terry:I'm trying to make up for past sins. The state says my three months in juvie wiped me clean, but my soul tells me different. Every time I put on that suit, it's my chance to help people that are in trouble. I guess on a personal level, it's a chance to look like a worthwhile human being again. In my eyes, if no one else's! It's what I want, Bruce.
Bruce: ...Stupid kid. You don't know what you want. None of you ever did.
[Terry stands, shocked, then angrily throws his Batsuit at Bruce's feet and storms out of the Batcave]
Possibly not a case of Bruce being lousy at relating to others. Considering Bruce later tells Terry it's he who makes Batman worthwhile and not the other way around, Bruce insulting Terry might be an example of Break His Heart to Save Him.
A small one near the end. When an aged Harley comes to get her granddaughters, the DeeDee twins (real names Deirdre and Delia Dennis). Harley is now fully reformed from her old villainous days and, if going by her dialogue is correct, has been raising her two granddaughters since they were young. And now they're both heading down the same dark path she did all those years ago. There's no clear indication if the twins will fully reform or not; and they just tell her to shut up when she calls them out for being ungrateful to their nana.
In a way, Joker shooting Bonk in front of the other Jokerz. Normally you'd think nothing of a Big Bad offing an incompetant minion, but the others are terrified not just of the Joker himself, but for their friend's sake. Chucko actually tries to stop Bonk from going through on his rant, which says a lot for how close these guys still are. Worse, Bonk gets shot for standing up to the guy verbally abusing his friends, further establishing what a bastard Joker is. It's brief, but it does serve to humanize these kids.
