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Tear Jerker: Batman Beyond: Return of the Joker
The last part of the original Joker's death scene. 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 the Joker's last words in the uncut version:
The Joker: That's not funny... That's not... *gurgles as he falls to the ground, the flag impaled in his chest*
Batgirl's reaction and her attempt to comfort Tim.
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.