When young Bruce falls down a well and breaks his arm, Thomas not only retrieves him, but he sets the bone himself.
After meeting Falcone, Bruce Wayne gives his coat to a homeless guy in an alley. As Bruce walks away, the homeless guy muses, "Nice coat." Later, when Batman takes out Falcone's henchmen, he notices the same homeless guy, and this exchange happens:
Batman: Nice coat.
Homeless guy: Thanks.
Alfred: "Why do we fall, sir? So that we can learn to pick ourselves up."
Bruce: "You still haven't given up on me?"
Then this one:
Commissioner Gordon: "I never said 'thank you'."
Batman: "And you'll never have to."
Echoed beautifully in The Dark Knight:
Batman: "You don't have to thank me."
Gordon: "Yes, I do."
And again in Rises:
Batman: "Don't thank me. Not yet."
Blake: "I may not get another chance."
While Batman scales the apartments, a boy goes out onto the balcony with the sound of loud fighting in the other room. This is in the middle of something rather important, but Batman not only pauses, he makes a sound to alert the boy to his presence. The kid is entirely unafraid, but when he resumes being crestfallen after realizing that no one would believe him, Batman tosses a gadget down and then resumes climbing.
Officer Jim Gordon putting his coat around Bruce on the night his parents are murdered and reassuring him that everything will be okay.
The Dark Knight
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. The kicker is the moment when the big threatening criminal 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.
Made even better by the look of 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 are 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.
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.
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'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 turns into a sincere speech 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.
The Dark Knight Rises
We've already got one from the second trailer, or what little we could from Alfred.
Alfred:: "Youíre as precious to me as you were to your own mother and father. I swore to them that I would protect you, but I havenít."
Not much, but judging from the look on Bruce's face, it's shaping up to be an defining scene for whatever Bruce decides to do.
The ending. All of it. From Bruce turning Wayne Manor into orphanage to John finding the Bat Cave in the final shot and, most of all, Alfred's happy ending - seeing Bruce and Selina happy and safe in Florence. It was an ending worthy of Shakespeare - one where everybody got what they deserved. And most of all, Bruce - he got to see the people he loved most of all happy.
Not to mention Jim finding the Batsignal on top of the MCU, repaired after all these years, and touching the bat symbol as if making sure its real because he knows who had to have repaired it.
And the unveiling of the Batman statue. It doesn't matter that the citizens of Gotham don't know who Batman really was. They honor him all the same.
This is made even more heartwarming when you remember The Joker's words to Batman: "They need you right now, but when they don't, they'll cast you out like a leper." Even though they no longer need him, they still choose to honor the man that he was and by doing so, once again, prove the Joker's philosophy of human nature wrong and Batman's correct.
The look on Jim Gordon's face at this moment. Compare it with his obvious torment at the beginning of the movie when honouring Harvey Dent's memory. Seeing Batman finally get the recognition he deserves as a hero clearly provokes a lot of emotions within him, but at the same time for what might just be the first time in all three movies he looks almost at peace.
Blake and Gordon's conversation at the end following Bruce Wayne's funeral. Blake bitterly comments that no one in the city will know who saved them. Gordon, clearly satisfied that wrongs have finally been righted, corrects him: "They know. It was the Batman."
The Reveal of Talia Al Ghul manages to simultaneously make you say "Oh, Crap" and "Awww!" Ra's Al Ghul's child, who escaped the inescapable prison, wasn't Bane but Talia. Bane was the one who helped her escape, sustaining the injuries that necessitated the mask as a result - she came back with the League of Shadows and rescued him, and he's been acting as her loyal servant ever since. The tender regard they show for one another as this is revealed is heartwrenching - which is amazing, given that they're simultaneously planning to string up Batman's corpse.
This also puts a new spin on Bane appreciating the boy singing the national anthem at the football game.
For all that happens later, Bruce's romance with Miranda/Talia is full of it. She helps bring him back into the world, and their Big Damn Kiss in Wayne Manor is pure heartwarming. When she suggests they run away together, and Bruce instead goes to fight Bane for the first time, it veers into Tear Jerker territory. Even knowing that he was responsible for her father's death, one can't help but feel that, for that moment, Talia honestly hoped Bruce would return her feelings, leave Gotham, and be the person her father wanted him to be.
The Ominous Arabic Chanting featured in the trailers whenever Bane was shown was actually encouragement for Bruce, climbing out of the pit.
The first set of inmates in the Pit were at the very least desperate and resentful, and refused to let even an innocent child escape, let alone help in the effort. The second set of inmates were still desperate and dejected, but they tried to help in the only ways they could. Even in desperate circumstances people can choose to be better; the second set of inmates already chose to defy Bane once and didn't completely surrender their ability to act nobly even in an even more desperate and bleak hellhole than the prison originally was.
Just before flying off to detonate the bomb, when Batman hints who he is to Commissioner Gordon (slightly paraphrased):
Batman: A hero can be anyone, even an ordinary man who does something as simple and reassuring as putting his coat around a terrified child, letting him know the world hasn't ended.
Gordon: ...Bruce Wayne?
Can be even better, as it shows that both of them remember that small act of kindness from probably around 30 years prior.
Another sweet way to look at it: Batman considers Gordon to be a hero to him.
On the meta side, there was speculation that Robin was too unrealistically bright, in all senses of the phrase, and would never make it into the grim, realistic Dark Knight Saga. Nolan and Bale themselves confirmed these rumors. But at the end of The Dark Knight Rises, John Blake is revealed to be a composite of Dick Grayson, Tim Drake, and Jason Todd. Not to mention his real first name is Robin. In the packed theater that this troper attended, everyone cheered.
A small one that's easy to miss. Bruce, after climbing out of the prison, throws a thick rope down to the inmates.
Also, the prison doctor, who'd befriended and supported Bruce, getting teary-eyed with happiness at Bruce's successful escape.
When Bruce escapes, the inmates all cheer.
And the fact that what they are chanting is simply, "Rise." Coupled with how they cheer, it shows just how much they wish for someone to leave the hell they lived in.
Batman is carrying a bomb away from the city to his death. His last words? Telling both Gordon and Selina that they are just as good as he is, and he has faith in them.
By showing up in the cafe with Selina, Bruce has not only forgiven Alfred for lying, but he has taken the advice to move on and be happy.