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.
Killer Croc is fighting Batman in a dark room, Joker then grabs Scarface's Tommy gun with the intent to shoot inside the room. Scarface (With the Ventriloquist) said out of concern that he might shoot Croc, while Joker didn't care. It's nice to see that the inmates do have some sense of concern for each other.
The ending offers a rare glimpse of hope that at least one of Batman's Rogue's Gallery can be redeemed. Harley Quinn is declared sane and freed from the asylum, eager to start a new life for herself. Unfortunately, the day is riddled with misunderstandings (none of which are really her fault), all sparked by Harley being a bit too hasty to take a new dress she bought out of the store (the sensor used to prevent shoplifting was still inside). Even when she accidentally kidnaps Veronica Vreeland, she still remains pleasant. The end of the episode finds her back in Arkham courtesy of Batman and Robin, who explain that Ms. Vreeland won't be pressing kidnapping charges against Harley, since it was just incidental and Harley had been nice about it. But the truly heartwarming moment comes when Harley asks why Batman tried so hard to help her stay out of trouble:
Harley: 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 are looking at each other in confusion at the scene.
Harley: (coy) Call me.
Batman: (smirking as he stays badass) Don't press your luck.
Immediately after, though, Ivy gives a sincere smile to Harley as she passes by - she had, after all, long advocated that she break up with The Joker and find someone who'd treat her right.
Read The Killing Joke and see how Batman reacts to Joker's "one bad day". To show such pity to Harley is so damn good.
The opening counts, too. When Dr. Leland tells Harley that she's passed her competency hearing and is going to be released the next day, Harley screams with joy, jumps out of her chair, and dances, clearly thrilled. She tries to amend her outburst, but Dr. Leland tells her to go ahead and celebrate—she's proud of Harley's progress. Later, even Batman offers Harley a handshake, congratulating her on her release.
Even Scarecrow gets in on the heartwarming moments in this episode. As he's being hauled back to his cell in Arkham by Batman and Robin, they pass Harley and Dr. Leland, and does something that suggests he really does care for Harley:
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, smiles and seems outright pleasant] Good evening, child. [Starts ranting again] Worship me, fools! Worship me! Scream hosannas of anguish to Scarecrow, the all-terrible God of Fear!
Dr. Leland gets another one in the ending: when Harley returns to Arkham, the psychiatrist assures her that with a little time and care, she'll be released again soon. It just goes to show that despite Arkham's status as a Cardboard Prison, there are people there who genuinely want to help their mentally ill patients get better.
The episode in general is heartwarming because it emphasizes that many of Batman's villains aren't necessarily bad people—they just suffer from a bunch of mental issues (to put it as politely as possible). It's a rare story that shows Arkham functioning as an actual hospital rather than a Bedlam House and while it's clear that Harley sadly has some serious problems that keep her from functioning in society it's also clear that there is hope not just for her but for other villains to be cured and rebuild their lives.
Even more Heartwarming in Hindsight, Batman's kindness and faith in Harley is ultimately rewarded in Return of the Joker, After the death of the Joker, Harley does reform. She has children, grandchildren, and lives to be an old woman.
When the inmates are testifying against Bolton, and Scarecrow, Harley, and the Ventriloquist are backed in a corner in terror, take a look at Crane: he looks like he's protecting Harley. Considering their interaction in "Harley's Holiday" mentioned above, even Jonathan Crane has a little humanity left in him.
Heck, even Batman's quote towards Bolton's actions;
Fridge Logic makes it even more heartwarming. Some fans might wonder why Batman isn't on Lock-Up's side, but then you remember that one of the inmates at Arkham used to be Bruce Wayne's best friend. Even after everything Two-Face has done, Batman still has hope that Harvey Dent can be redeemed. It makes perfect sense that he can't stand to see the inmates treated without hope or compassion.
"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 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 Crossover 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.
"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 Gray 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 marvels that the cave looks just like the Gray Ghost's Lair. Batman, with a smile, says he wants to show Trent something and takes him to 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 combined with Trent's ability to provide all the lost reels helped propel Trent back to wealth and 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, using the exact same words he said 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 Gray 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.
Also as Nostalgia Critic said, towards Bruce watching the show as a kid "It's nice to actually see a happy moment from Bruce's childhood"
Bruce: You know, as a kid I used to watch you with my father. The Gray Ghost was my hero. Gray Ghost: *Look of recognition* Really? Bruce: And he still is.
In a Christmas themed comic, Justice League Unlimited #28 Superman reveals that he watched the show as a child which means Simon Trent inspired, not one but two iconic superheroes to take up the cape.
But the best part by far is that the character's legacy lives on. In 'Arkham Knight', located around the city (but mostly at Panessa Studios) you can find posters for 'THE GHOST IN GRAY', a movie featuring Simon Trent playing the lead role, and the figure on the poster even looks like the Gray Ghost. Not only that, but in 'Lego Batman 3', Adam West returned to voice several characters, including the 60s version of Batman, and even the unlockable secret character of the Gray Ghost. This episode was so influential on the Batman mythos it's practically become as cemented as any other detail, such as the Zorro movie or the bat-phobia that Bruce has.
The end of "Robin's Reckoning: Part 2" (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 to 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 "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.
"Paging the Crime Doctor": Bruce Wayne pays the legal fees for a disgraced "mob" doctor who is also the brother of Rupert Thorne and only asks for one thing in return.
Bruce Wayne: Tell me about my father.
Even better is Dr. Thorne's reaction. At first he assumes Bruce wants something illegal and refuses his offer for help—but when Bruce explains that he simply wants to know more about his dad, Dr. Thorne lights up. Thomas Wayne (Bruce's dad) was Dr. Thorne's friend, so this isn't just Bruce learning about his dad...it's a man getting a chance to talk about his friend to his friend's son.
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, just as long as it's not a hacksaw. For the very abrasive Detective Bullock, even such a minor thing is a Heartwarming Moment.
The epilogue is one, too. Jim Gordon is shown sitting inside a nondescript diner on a street corner in Gotham, with the place's sole waiter commenting that "he's not gonna show up" and Gordon calmly denying it. Suddenly, the door swings open—it's Batman. It turns out that he and Commissioner Gordon have a yearly tradition: they meet in the same booth of the same diner at midnight on every New Year's Eve to have a cup of coffee and toast surviving another year. There's something extremely sweet about seeing two men who spend every waking moment of their lives defending people taking the time to appreciate each other's friendship.
In the comics based on the cartoon, the Penguin becomes the Mayor of Gotham and orders an all-out assault on Batman and his vigilante activities. Come New Year's, Gordon's still sitting in the same spot, mourning the fact that he won't see his friend this year, because he'd have to arrest him. Something distracts him and, when he looks back, there's a half-empty cup of coffee sitting across from him.
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 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!
Sid "The Squid", a bungling failure who's considered a useless joke in criminal circles (not to mention he's far too nice and meek to make an effective criminal even if he wasn't a clumsy doofus), is taken to jail at the end, only to find that he now has a massive rep for almost offing Batman, as well as getting the better of The Joker AND Rupert Thorne. That's all he ever really wanted.
Leslie: This used to be a beautiful street. Good people lived here once.
Batman: Good people still live in Crime Alley....
During "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, the employee can stay and work at Wayne Enterprises as long as he wants.
Not sure if it's silly or not, but this particular troper always found the giant teddy bear that says "I love you very much" in "Christmas with the Joker" ridiculously cute.
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?
Nightwing: You know me, always happy to have a little help.
During Dick's graduation ceremony, Alfred says he's very proud of Dick because he's like a second son to him.
"Double Talk" was one of the few episodes that allowed a member of Batman's rogues gallery a happy ending. The Ventriloquist, a criminal with multiple personalities, is dominated and bullied by Scarface, a ventriloquist dummy thats really a split personality acting through the dummy. By the time Double Talk rolls around, the Ventriloquist (real name Arnold Wesker), is seemingly cured and released from Arkham, but relapses through a series of events that turns out to be the work of two of Scarface's former henchmen who wants Wesker to relapse to get their leader back. Wesker does relapse, but Batman tries to help him the whole time, and when the final confrontation occurs, pleads with Wesker to realize that Scarface isnt in control, Wesker is.
Batman: *after knocking Scarface off Weskers arm with a batarang* Arnold, dont do this!
Arnold: *reluctantly picks up Scarface's machine gun* It's-it's out of my hands!
Arnold: ...Yes! *turns and shoots the dummy, knocking it into an air vent where it's shredded to dust*
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 (cut to Batman watching as the baby's mother sobs with joy as she hugs her child) 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.
To elaborate, the plot in general is Batman trying to convince mob boss Arnold Stromwell to turn his life around, to close his organization and to help the police stop the crime in Gotham by showing him how much his actions damaged his family. Seeing the Caped Crusader trying to convince a criminal to repent instead of beating him up for his informations is strangely heartwarming. The last part of the episode, while also a Tearjerker, has Stromwell reuniting with his brother, now a priest. The latter manages to finally convince him to do what Batman asked. At the end, Stromwell is shown talking to Gordon, to give him informations about Gotham's underground. It is implied that he then surrendered himself to the Gotham Police. He probably went in prison afterwards, but is now at peace with himself.
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.
Two-Face is deeply saddened that he feels like he can't be with his fiance' anymore,and his two Mooks seem legitimately worried about how depressed he is, encouraging him to try and see her again and even volunteering to pick her up and bring her to him. Even better, Two-Face later takes them up on their offer and they actually do it with no catch whatsoever. They don't threaten her or use her as leverage against Two-Face for money or anything like that. They just take her to Two-Face's hideout so they can be together again. A rare HeartwarmingMoments for some generic Mooks of all characters.
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 ultimately go their separate ways.
Joker: (pulls Harley close) That's okay, poo. I know you're a one-man loon.
Harley: (squeal of delight)
At the end of "The Forgotten", Bruce Wayne finds the two men he befriended in the labor camp, one of whom helped him remember who he was. Both had been duped into being imprisoned because they had been out of work and needed the money. After he reveals his identity, he tells them both that they should stop by Wayne Enterprises the next morning to start their new jobs.
A Real Life moment for actor Kevin Conroy. After 9/11, he was volunteering in a kitchen preparing meals for rescue personnel. 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 had grown up watching BTAS. The actor noted feeling humbled and honored.
According to Conroy, that fellow volunteer recognized everyone was so tired and downtrodden they needed some cheering up, and having the voice of Batman in their presence was perfect. So Kevin does his big recitation, everyone lights up and starts talking, and the fellow volunteer leans in and says "How's it feel to be Santa Claus?" And in context, Kevin absolutely agreed, "I felt like Santa Claus that day."
Harley's relationship with Bud and Lou, Joker's pet hyenas. She treats them just like a pair of beloved dogs (to the point of calling them her "babies"), feeding them, playing with them, walking them, and in return, they act like a pair of loyal pups around her. In contrast, they snarl and snap at almost everyone else, even the Joker, like you'd expect a pair of undomesticated animals to act.
In "Joker's Favor", Commissioner Gordon is less than happy at receiving a testimonial dinner. He argues that Batman should be receiving this honor, but Batman humbly declines ("I'm just the nightshift") and points out that it's Gordon who protects Gotham 24/7. At the Dark Knight's encouragement, Commissioner Gordon decides to accept it.
Batman has a supporting presence for most of the episode, since Charlie Collins is really the protagonist. Still, when Batman and Charlie finally meet, the Dark Knight is nothing but sympathetic towards his plight and what The Joker put him and his family through.
In "The Cape and Cowl Conspiracy", Josiah Wormwood is defeated and sent to prison, but Batman sends him a package. The note reads, "Confinement will speed your reform, but long, cold nights will be the norm, so here's a thing to keep you warm." Inside is a copy of Batman's cape and cowl. Sure, Wormwood throws it aside in anger, but who imagined Batman would do that?
"See No Evil", concluding with Batman coming to talk to Kimmy and make sure she's all right after her ordeal.