In the climax (that is to say, the second one), when both ferries choose to spare the other. After watching the Joker's nigh-unstoppable killing spree for the past two hours, seeing his Humans Are Bastards view proven wrong is a real thrill. Two kickers is first off, when even the businessman who tries to insist on killing the criminals finally realises he just can't do it himself and nobody else will either, and then the moment when the Scary Black Man took the detonator, saying "I'm gonna do what you should have done ten minutes ago," and then throws it out the window, then sits down again. And none of the other prisoners even protest. Rousseau Was Right indeed.
Made even better by the disappointment on The Joker's face when he realizes he was wrong.
"What were you trying to prove? That deep down, everyone is as ugly as you? You're alone."
Jim Gordon reuniting with his wife after he was presumed dead.
Also, at the end when Batman :willingly decides to be the hero Gotham deserves, and the villain it needs.
Plus the closing speech by Gordon.
Son: Why's he running Dad? Gordon: Because we have to chase him. ...Because he can take it. Because he's not our hero. He's a silent guardian. A watchful protector. A dark knight.
The moment after Bruce Wayne saves Coleman Reese, Reese is being escorted out of the police vehicle by Gotham police as Gordon talks to Wayne. When Wayne fakes confusion and ignorance of what's going on, even asking who's in the car that he "supposedly" saved, he looked right at Reese, who has an expression of pure disbelief on his face, and gives him the tiniest of nods.
A meta-fictional example is when Heath Ledger was awarded a posthumous Academy Award for "outstanding actor in a supporting role". His family, including his father Kim, went onstage to accept the statuette on his behalf. Kim said that Ledger's young daughter Mathilda would inherit the Oscar when she turns 18. Not a dry eye in the whole Kodak theatre.
A well-circulated narrative that went around between Ledger's death and the film coming out was that Ledger "lost" himself in The Joker, that Method Acting as The Joker eventually led to his demise. While it was true Ledger holed himself up in a motel for a few weeks to circle in on nailing on the character, everyone who worked on the movie spoke the world of Ledger as a person and co-worker, and there's footage of him mingling with the crew and skateboarding on set. Michael Jai White, who as Gambol worked in two scenes with Ledger, said Heath easily slipped in and out of the Joker depending if the cameras were rolling.
The Dark Knight Rises doing a silent treatment of The Joker. No recasts, no bus crashes, not even a throwaway line acknowledging Gotham's triumph over him - so as to not diminish Heath Ledger's memory.
The scene before the press conference where Batman is supposed to turn himself in. Bruce is contemplating turning himself in and admits he can't handle the situation with the Joker to Alfred.
Bruce: Today you get to say I told you so.
Alfred: Today... I don't want to.
(As they walk away together)
Alfred: But I did bloody tell you... I suppose they're gonna lock me up as well as your accomplice?
Bruce: Accomplice? I'm gonna tell them the whole thing was your idea.
Bruce Wayne's speech to Harvey Dent. At first it seemed like he was trying to humiliate the poor guy in a hazing manner, as expected from his Rich Idiot With No Day Job persona. However, it soon turns into a sincere speech expressing his faith in Harvey Dent being the symbol of hope Gotham needs, as if the little boy who lost his parents just dug himself out of that persona to give him personal thanks for restoring his faith in the justice system.
Rachel: Harvey may not know you well enough to know you're making fun of him, but I do.
Bruce: No, I meant every word.
Batman not wearing hockey pads pretty much is the exact reason why he doesnt like the copycats - he has seven years of training and high-tech equipment, but the copycats only have nylon padding, Halloween masks, and guns. Based on his conversation with Alfred later, Bruce would prefer being the only person putting himself at risk every night.
Alfred: Why dont you hire them and take the weekend off?
Bruce:[laughing] That isn't exactly what I had in mind when I said I wanted to inspire people.