And to drive home the Tear Jerker in this scene, imagine what's going through Bats' head at that moment. Over the course of B:TAS, Batman'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 Bats can feel much emotion at all without being driven to his breaking point. Now which is the greater Tear Jerker in this scenario: the Joker mindraping 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?
Batman might have felt Unstoppable Rage during that scene, considering he throws a knife at the Joker's head which Joker barely dodges and threatens to break Joker in two.
While some consider Harley Quinn going along with the 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 the Joker's accomplice as he tortures and Mind Rapes Tim into Little J. It's yet another painful note on their twisted sad relationship and another display of how the 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 Mind Rape and somehow salvage him into an adopted kid.
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 in the series, 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 getting hurt when the Jokerz attack her and Terry. Poor girl is nearly killed and has absolutely no idea why.
When Bruce forces Terry to give up the bat-suit, he's trying to protect the boy but he's so lousy at relating to people that he can't say what he wants.
Bruce: (looks at the case holding the bat-family suits) I had no right to force this life on you or anyone else.
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: (shocked, Terry angrily throws the suit at Bruce's feet)
A small one near the end. When an aged Harley comes to get her granddaughters, the DeeDee twins, (real names Deirdra and Deila). Harley is now fully reformed from her old villainous days and, if going by her dialogue is correct, has been raising her two grandkids since they were young. And now they're both heading down the same dark path she is. There's no clear indication if the twins will fully reform or not.