In "Trial", Gotham District Attorney Janet van Dorn spent the entire first half of the episode haranguing Batman under the belief his vigilante justice had made the crime in Gotham worse. After being forced to defend him in a sham trial, at the end of the episode she acknowledges his effectiveness in fighting crime.
Janet: I see now there's a need for the things you do. But I'm still going to work toward a city that doesn't need Batman.
The end of the episode "Harley's Holiday, " which offers a rare glimpse of hope that at least one of Batman's Rogue's Gallery can be redeemed; after the stress of a bad day riddled with misunderstandings (none of which were really her fault), Harley had actually reformed, but was a bit too hasty to take a dress out of a store after paying for it. The end of the episode finds her back in Arkham courtesy of Batman and Robin, who explain that Ms. Vreeland wouldn't be pressing kidnapping charges against Harleen, since it was just incidental and Harley had been nice about it.
Harleen: There's one thing I gotta know. Why'd you stay with me all day, risking your butt for someone who's never given you anything but trouble?
This was then followed up with a nice peck on the lips... and Harley liked it enough that she flung the dress away and kissed Batman for about 6 seconds in front of an uncomfortable Robin and Poison Ivy, who's looking just as confused as anybody.
Harley: (coy) Call me.
Batman: (smirking as he stays Bad Ass) Don't press your luck.
Related, that moment in the episode "Lock-up" where Bolton realizes that Batman cares about his rogues.
"The Underdwellers" is a notable episode for showing Batman in full-on Papa Wolf mode - don't ever harm children on his watch. The Sewer King is a verbally abusive tyrant who keeps child slaves underground, and orders them out into the night to bring him food and valuables. Batman shows seething disgust when he finds the hellhole they're kept in, and tells them what's what with one symbolic gesture: he loudly rings the bell usually used by the Sewer King to summon all his minions, and once everyone's in the room, he rips the bell off, letting it slam to the floor. And then tells the children this:
Batman: I don't know what kind of barbarian did this to you, but it's over. And from now on you'll be treated like human beings.
And that's not the most heartwarming moment. After Batman successfully captures the Sewer King and seriously chews him out - a Crowning Moment Of Awesome for Batsy - the Happy Ending shows the children being rescued by the police, and seeing the sunlight for the first time in ages.
The ending of Batman & Mr. Freeze: Sub Zero. If you've seen Batman: The Animated Series, or even read its entries on the Tear Jerker page, then you should know about how the tragedy of Dr. Fries's wife's illness and then apparent death turned him into the tragically emotionless Mr. Freeze. Partway through the series, it's revealed that his wife is still alive, and Freeze spends the movie trying to get organ transplant for her in order to save her life. After an apparent case of Redemption Equals Death, Nora's body is saved, and, on the news at the end of the movie, we are told that not only has Nora been treated for the illness that would have killed her, but, as the camera turns away to reveal Freeze watching at the television through a window in the Arctic, his cryogenic research that turned him into Mr. Freeze saved her life, and she is now in stable condition. As Fries cries tears of joy, so does the audience, and, at that, Fries trudges through the ice and snow to nowhere in particular, just happy that Nora is alive and well. It's a shame The New Batman Adventures came and screwed all that up.
Seriously. That was the perfect ending to that storyline.
"Meltdown" gave the story some closure which, while not being as heartwarming as the end of Subzero, does provide one last humanizing moment for Fries.
And the series itself has a few too. One in particular is the scene at the end of "Over the Edge" when Batgirl is about to tell her dad about her "new job", and he interrupts her and says (paraphrased) "You don't have to tell me, honey. No matter what you're doing, I love you." Awwww.
Made even sweeter when the episode heavily implies he already knows what "job" she is talking about (her being Batgirl) and that he is proud of her anyway.
There was also the Cross Over episode "Showdown," right at the end when Ra's Al Ghul finishes his story and reveals that the now-senile Duval is his son.
Ra's: "We will cross swords some other day. For now... let me take my boy home."
The ending of the episode Harlequinade is perhaps one of the most unusual examples since it's a heartwarming moment regarding The Joker. Yes....that Joker.
Sure, it's just so that Joker can manipulate Harley further, but Harley's happiness at the moment makes it worthwhile.
That's HIGHLY debatable. It's also possible that he loved how she had just been perfectly willing to kill him, since it reminded him she was just as crazy and murderous as he was.
"Beware the Gray Ghost". Simon Trent was an actor who played a costumed hero on TV which ruined his acting career by being forever typecast (appropriately enough, he is voiced by Adam West). Trent can't get a job because no one will take him seriously, and the Grey Ghost has long since gone off the air. He has to sell all the collected props and memorabilia he has (which showed he had fond memories of the show despite it ruining him) just to pay the rent. When Batman comes to him for advice for a mad bombing case, Trent reluctantly points Batman in the right direction (the bomber was aping an episode of the old show), he later decides to put on the costume and help Batman out. When he's taken to the Batcave, Trent finds a small room, filled with Gray Ghost memorabilia (Bruce was an avid fan when he was a kid). At that point, Trent learns that for all the show had done to him, he had at least inspired someone to do real good: "So it wasn't all for nothing." At the end, we see that because Trent as the Gray Ghost helped Batman, a renewed interest in the Gray Ghost franchise helped propel Trent back to stardom (the legacy of which lasted all the way to Batman Beyond). As a further reward, Bruce clues him in on his secret (he went to the VHS signing as Bruce Wayne and told him how he was a big fan when he was a kid, saying it exactly the same (minus Batvoice) as he said it to him while in the Batsuit).
What's better? After Trent sells all the memorabilia Batman buys it and returns it to him.
This also can count as a real-world Heartwarming Moment because of Adam West's role in the episode. As one person put it: "It was the show's way of saying that if that cheesy superhero hadn't existed, this show probably wouldn't have existed."
There's a meta CMOH, as well; the creators of the episode stated that if they hadn't gotten West to voice the character, the entire episode would have been scrapped.
Seeing the point where Bruce is watching the Grey Ghost episode and suddenly starts sporting this childlike grin on his face. There's a look in his eyes, and suddenly he's a child all over again. It's amazingly touching.
The end of "Robin's Reckoning", part two (despite the fact that it's nowhere near as good as part one.) Batman has gone after the people responsible for the death of Robin's parents, and has been cold and distant with him for the entire ordeal, leaving him behind and not revealing to him what was going on. By the time they finally get a chance to talk about it, they've had two screaming arguments, Bats is injured and in a makeshift leg-splint, and Robin's both accused Batman of heartlessness and come within a few inches of killing the crook. As Gordon is dragging away the villain and his mooks, they have a quiet conversation on the docks as the sun rises:
Robin: "You were right, y'know - not bringing me along. You knew I'd take it too personally.
Batman: "...It wasn't that, Robin. It wasn't that at all." (limping) "Zucco's taken so much, caused you so much pain. I couldn't stand the thought that he might... take you, too."
Alfred's response when Bruce tells him about the visions of his father Scarecrow's toxin's been causing in "Nothing to Fear":
Bruce: He says I'm shaming the family name.
Alfred: That's rubbish, sir! I know your father would be proud of you because... I'mSo Proud of You.
In the episode "I Am The Night," Batman is having severe self-doubt issues and wonders whether the neverending war he wages is worth it. These feelings reach a critical level when Commissioner Gordon is shot during a raid that Batman was supposed to help with, but arrived late to because he was visiting the site of his parents' murder. Harvey Bullock shouts at Batman that he's just as guilty as the men who shot Gordon, and Batman lies in crushing despair for days. Finally, when the man who shot Gordon escapes from prison, Robin pulls Batman out of his misery by reminding him of what he stands for, and Batman arrives just in time to save Gordon's life (in a Moment Of Awesome, no less). Jim wakes long enough to deliver one of the biggest Heartwarming Moments of the series:
Jim Gordon: Got to keep fighting. Never stop. What I try to live by. Maybe if I'd been younger, I could've been like you. Always wanted to be a hero.
Batman: *following up one Heartwarming Moment with another* You are a hero, Jim.
When the guy Batman saved earlier - who had berated him at the time - thanks him at the end of the episode and tells Batman that, because of him, the guy is getting his life together. See, Batman? You do matter.
Bruce Wayne pays the legal fees for a disbarred doctor who is also the brother of Rupert Thorne and only asks for one thing in return.
Bruce Wayne: Tell me about my father.
In the Batman-Superman story, Lois discovers that Bruce Wayne (whom she is dating at the point) is Batman. As she tends to his wounds, she bemoans how she is sitting atop the biggest story in history, the true identity of Batman, yet there's "not a blessed thing" she can do about it. Bruce smiles at her and says
Bruce Wayne: Then you really do care about me?
A strange moment occurs in "Holiday Knights" when Harvey Bullock is on a stakeout where has to pose as a mall Santa. There he meets the daughter of a man he put in prison who innocently asks him (or rather, Santa) to bring her (imprisoned) daddy home. Bullock, instead of being rude and nasty like he was to the other kids, softens up and gives the girl some money so she could buy herself a present. when she asks if she can get one for her dad, he said she could, so long as it isn't a hacksaw. For the very abrasive Detective Bullock, even such a minor thing is a Heartwarming Moment.
In The Man Who Killed Batman, Joker goes into mourning over the apparent death of his nemesis, setting up an improvised funeral and admitting that crime is no fun without Batman to show up and stop him. Being the Joker, he immediately turns that heartstring-tugging into a Funny Moment:
Joker: Well, that was fun. Who's up for Chinese?
A much more genuine case of heartwarming for the episode comes from Bullock of all people. Too bad Bats couldn't see how truly devastated the crusty old detective was when he thought there was no more Batman. D'AWWWW!
There is also the Throw the Dog a Bone moment at the ending where the prison inmates respect Sid the Squid for at least almost offing the Batman.
The mayor being reunited with his son at the end of "Be a Clown."
Batman covertly returning Isis to Selena in "Cat Scratch Fever."
Batman and Leslie Thompkins paying respects to Bruce's parents.
Leslie: This used to be a beautiful street. Good people lived here once.
Batman: Good people still live in Crime Alley....
During the episode "Mean Seasons", the B-story is about an employee at Wayne Enterprises who is being forced into retirement (having hit the mandatory maximum age). Bruce Wayne calls the despondent employee into his office and mentions that he won't be coming to the retirement party...because it's being canceled, along with the mandatory retirement policy. Bruce then tells him that, as far as he's concerned, he can stay and work at Wayne Enterprises as long as he wants. It's moments like this that show no matter how far into the shadows Batman goes, there's still a lot of light left in him.
The ending of "Old Wounds", even though much of the episode was a Tear Jerker. It starts with Nightwing helping Robin take down a couple of guys who were stealing wallets. The flashback that takes up most of the episode has a part where Batman interrogates one of the Joker's lower goons in front of his frightened wife and child. This was one part of what drove Dick to quit being Robin, and he explains at the end that he hasn't forgiven Batman because he claims the latter will never change. Then he discovers that one of the wallets belongs to the man that Batman had questioned. When they go to return it, they find that his confrontation with Batman had driven him to go straight and get a job as a security guard for Wayne Industries, where Bruce Wayne always takes the time to stop and ask him how his son is doing.
Robin: Guess Batman had a change of heart. Who'd have thought he had one?
(They see the Bat-Signal in the sky)
Robin: Speak of the devil. You coming?
Nightwing: ...I guess it's about time.
The exchange between Batgirl and Nightwing in "You Scratch My Back".
Batgirl: You alright?
Nightwing: You know me, always happy to have a little help.
"Double Talk" was one of the few episodes that allowed a member of Batman's rogues gallery a happy ending. The ventriloquist dominated by seemingly sentient puppet Scarface, Wesker, is released from Arkham and given a job at Wayne Enterprises along with a place to stay. However, events occur which allow Scarface to surface again. Batman manages to talk Wesker down from following Scarface's orders, who gets rid of the puppet for good. The end shows Wesker shaken, but recovering. And the icing on the cake? Throughout the episode, Batman has been helping Wesker by getting him the job (as Bruce), and attacking the thugs harassing him (as Batman).
From the related comic series here: Batman has rescued a baby whom some Russian general implanted the launch codes of several nuclear weapons into his DNA. Because of the Possibility of Ra's coming after the codes, Batman decides that he has to keep the child with him. He never stops doing his usual rounds. He pulls it off well, even though he gets lectured on how to properly hold the baby by both a woman he rescued from muggers and the muggers. In the end, Batman turns over what is supposed to be the kid's blood sample to the FBI. Only he switched it with his own, figuring that when they failed to find the codes, they'd assume it was a red herring and all parties involved would call off the hunt. When asked about the possibility of the FBI using the sample to find out his Secret Identity, he simply says:
Batman: "If I had to choose between my identity becoming known, or Kristov having a normal life with his parents... that's no choice at all."
The ending of "It's Never Too Late," where Batman manages to get a mob boss to turn state's witness in order to repair his relationships with his family
The moment in "Perchance To Dream" when Bruce Wayne decides to accept that he isn't Batman, and hugs his dad. It turns out to be All Just a Dream, but it's still heartwarming to see Bruce so happy.
In Two-Face's origin, while Batman is pouring over scores of psychology books:
Scarecrow is being hauled back to his cell in Arkham by Batman and he goes past Harley's competency hearing:
Scarecrow: I am the Master of Fear! The Lord of Despair! Cower before me in witless terror!
Harley: Hi, Professor Crane!
Scarecrow: (instantly calms down and seems outright pleasant) Good evening, child. (Starts ranting again) Worship me, fools! Worship me! Scream hosannahs of anguish to Scarecrow, the all-terrible God of Fear!
You see, no matter how crazy Scarecrow is (and he might just be putting on a show for Batman), he does care about Harley.
Harvey is being hauled back to Arkham, when he stops and sees Bruce Wayne and Dick Grayson nearby. Harvey smiles and says the following to Bruce, reminding you of the fact that they were once close friends:
Harvey: Bruce...Good old Bruce. You were always there. You never gave up on me.
Followed by Dick pointing out Harvey was right, that Bruce still had hope for Harvey's redemption. Followed by Bruce pointing out Dick was always there for Bruce as well. This part becomes a Tear Jerker though when you realize that, one day, Dick and Bruce have a falling out and go their separate ways.
A Real Life moment for actor Kevin Conroy. After 9/11, he was volunteering in a kitchen preparing meals for rescue personal. When another cook learned that he was the voice actor for Batman, he was encouraged to go into the cafeteria and recite his famous line ''I am Vengeance! I am the night! I. AM. BATMAN!!'' After being greeted by cheers and applause, many of the rescue personal told him how they watched Batman: The Animated Series growing up. The actor noted feeling humbled and honored.