In the The Spectacular Spider-Man episode "First Steps", two kids poke fun at a little girl's sand castle. Sandman uses his power to turn the area around them into a huge Disney-esque castle, chasing the boys away. The little girl thanks "Mr. Sandman". He smiles and tells her to go home as its getting cold. The episode is Pet the Dog from beginning to end.
Bender on Futurama petted the dog a few times, but the show spoofed this on at least one occasion:
Bender: But inside, you've got the heart of a robot. Fry: Aww... thanks, Bender. Bender: Just like inside me, I've got the heart of a human! (takes a human heart from his chest compartment) ...What?
Bender's biggest Pet the Dog moment was most likely in "Jurassic Bark", where he spends the whole episode acting like a insensitive, possessive, abusive, jealous jackass because Fry, his best friend, is spending so much time trying to figure out how to clone his old dog Seymour, his best friend before Bender. Eventually, Bender gets so fed up he takes Seymour's fossil and throws it into a lava vent. However, when this causes Fry to collapse in grief, he realizes (and admits), that Fry loved his dog much the same way Bender loves Fry. He then dives into the boiling lava to retrieve Seymour despite Fry's protests, melting his eyes in the process.
Virtually any time Bender realizes he seriously hurt Fry's feelings leads to him showing unusual kindness.
Stickybeard: Say, lassie, would ya mind keepin' this business of savin' ye secret from the other villains? They wouldn't invite me to next year's barbecue if they found out...
Also, in "Operation: B.U.T.T.", Numbuh One quits the team for no apparent reason, and Numbuh Four is so upset, he yells at Numbuh Three, inadvertently making her cry. In the next scene, however, he's trying to cheer her up with her stuffed animals - meaning this is really big, because he's usually finds her stuffed toys sickeningly sweet. (He doesn't do a very good job cheering her up, but fortunately, everyone cheers up when they find out just why Numbuh One quit. (The Delightful Children had taken a photograph of his bare butt and were blackmailing him; they really couldn't help but laugh.)
Rampage from Beast Wars is generally depicted as nothing short of a monster, a sadist, and a walking nightmare...except in the episode "Transmutate", in which he finds a kindred spirit in the episode's freakish, disfigured, and pitiful title character. He even goes so far as to be moved to sorrow by its death.
The trope can apply to pure villains as well. In Justice League Unlimited, Galatea, the murderously psycho clone of Supergirl, shares a moment of genuine warmth with her "father", Professor Emil Hamilton, just before she cheerfully goes on a mission of mass murder.
Azula gets a couple during the Beach Episode, such as when she makes a cutting remark towards Ty Lee about how she only attracts so many men because she is such a tease, and then apologises when Ty Lee cries (even admitting that she is a bit jealous). This goes some way to showing that Azula's friendship with Mai and Ty Lee does mean something to her which foreshadows the effect that their Heel-Face Turn has on her.
Azula is also remarkably non-lethal most of the time and usually puts her defeated enemies in jail while you expect a pure villain like her to kill them off.
The Warden was a one off villain in the Boiling Rock episodes. He was shown as demeaning, and somewhat sadistic in the way he treated prisoners, and a man so devoted to his job, he'd consider suicide over letting prisoners go. When Zuko was captured, he chastised him, not only for being a traitor, but also for breaking his niece's Mai's heart. After Mai get's free in the end, she explains that one of the reasons that she was out was because the Warden pulled some strings for her despite the fact that she was instrumental in causing a prison escape.
The Monarch in The Venture Bros., tears up moments before he was to be declared man and wife with Dr. Girlfriend. The Phantom Limb interupts the wedding with copters which prompts the Monarch to scream "OHHHH, DICK MOVE!"
The Monarch pet the dog so hard in season two, that fans were actually upset to be reminded in the following season that he is, in fact, a professional villain, and therefore not very nice.
Dr. Venture Sr. is often depicted as an emotionally abusive and negligent father. However, in the episode Spanakopita, after tracking down the Greek islanders who stole from his boat and inadvertently kidnapped Rusty, he sent his son away and he and his friends promptly beat the crap out of the people who robbed him and planned to ransom his son.
Stewie Griffin, in the early seasons of Family Guy, was a diabolical and downright sociopathic baby who, after petting the dog a few times, had his character changed completely by the fourth and fifth season. But who are we kidding? It's alljustforlaughs.
Another Family Guy episode offers a subversion when greedy tobacco company executives discuss making a line of toys to get kids interested in smoking cigarettes, complete with an Evil Laugh. Until the head pulls up a puppy and starts to pet it and talk to it in baby voice. He then hands the dog to another executive, pulls out a rifle and says "Pull..."
In a more sentimental version, Mayor Adam West is a total lunatic but his romance with Meg is genuine, and when Meg tells him that Brian plans to expose it, Mayor West decides to break up the relationship to protect her. Brian who saw this, is deeply moved and tears up the photo.
Invader Zim has a few Pet the Dog moments with his minion-disguised-as-a-dog.
Gir:(tearing up after Zim yells at him) Zim: Guh... I can see you understand your mistake, Gir, and me being angry will get us nowhere.
Zim also promised the moon to GIR once he takes over Earth and genuinely worries about him during a zombie (candy-starved children) attack.
Zim: Maybe that little robot isn't such a bad evil minion after all.
In The Boondocks, Uncle Ruckus, a black man coincidentally racist against other black men and a white supremacist, is shown petting the dog many times (excluding all of the times has talked to Granddad), namely in the episodes "The Trial Of R. Kelly" (the park scene), "Granddad's Fight" (Ruckus is willingly Granddad's co-sensei, and comments after the fight with Stinkmeaner: "I told you a nigga that black couldn't fight."), "Return Of The King" (where Ruckus comes to dinner with Granddad even after throwing random objects at Martin Luther King), "The Itis" (where Ruckus comments: "If there's one thing a colored man is good at, it's cooking up a pig."), "Stinkmeaner Strikes Back" (Ruckus helps Huey, Riley, and Granddad exorcise Tom), "Home Alone" (Ruckus agrees to babysit Riley and Huey), and "The Story of Catcher Freeman". (Ruckus comments: "Catcher Freeman was the greatest nigga that ever lived!")
And none of those cover the most notable and most genuine act of dog petting Ruckus ever did, in the Christmas episode; after filling in as a mall Santa and leaving Jasmine completely disillusioned when it comes to Santa's existence, Ruckus later approached her and explained that of course he wasn't really Santa, but he was, in fact, a Secret Service agent assigned to fill in for Santa, as Santa needed to be protected from the threats against him (namely Riley Freeman and his paintball gun). Ruckus then assured Jasmine that the real Santa would be back next year, much to her delight. It's a surprisingly genuine and heartfelt moment which, since it's The Boondocks, is immediately subverted by Huey's narration where he impassively observes that Christmas miracles "only come from the lies adults tell children."
Played with by the Joker on Batman: The Animated Series and his relationship with Harly Quinn. Almost any time he shows real affection towards her, you can tell that he is just using her as another part of his mind games. She would catch on that he doesn't really love her, and all it took was a token gesture of affection and she would melt in his arms again.
Eventually expanded upon in the comics, where the Joker actually does have feelings for Harley, but his insane mind alternates rapidly between being attached to her (leading to Pet the Dog moments), not really caring about her (leading to Kick the Dog moments), or having feelings for her but hating the fact that he does (leading to some really bad moments), which all in all adds up to one screwed up relationship.
Joker gets a good, if twisted, one in "Emperor Joker," as he's preparing to use Mxyzptlk's powers to destroy the universe, Harley tries to talk him out of it, so he explains his surprisingly sympathetic motives (he believes any universe where a person like him could exist is fundamentally screwed up and needs to die), and then turns her into a constellation so she go peacefully and light the sky at the end of the world. He then proceeds to brutally murder everyone else (by which we mean everyone else) but the whole thing is surprisingly sentimental given that it's the freakin' Joker.
"Say goodnight, Harley. I always wanted to see my dame in lights. Heh. Even in a moment of abject saccharine, I still got it."
Subverted in Batman Beyond: Return of the Joker. The Joker and Harley look like they're setting up for one when they tell Batman and Batgirl that they've given up their lawless ways and just want to settle down and start a family. Then wefind who "Joker Junior" is to be played by...
Batman Beyond: The temporarily reformed Mr. Freeze saves a cat from falling in the track of a speeding subway and gives it back to a grateful little girl and her family. Mr. Freeze was about as anti as an Anti-Villain could get already. He makes his first appearance in Batman Beyond expressing a desire to help people out. He even starts a charity to right the wrongs he committed, naming it after his beloved, dead wife.
In two Ben 10: Alien Force episodes in a row, a featured villain (Charmcaster and Vilgax) save the life of a child (Charmcaster levitates a boy away from being hit by a truck, and Vilgax defends one of his species' children from Ghostfreak's minions.) The two still engage in evil-doing afterwards, though.
In Transformers Animated there are very few moments where Sentinel Prime acts less of a Jerkass, notably in "Return of the Headmaster" where he shakes Optimus' hand after helping him regain his stolen body, and "Predacons Rising" where he took some responsibility for what happened to Elita-1 (It was his idea to go to the planet where that event happened in the first place). But his biggest Pet the Dog moment to date was at the end of "Decepticon Air" where he offered Optimus a spot in the Elite Guard, showing that the two Primes have buried the hatchet.
In an episode where cats are banned from the town (because kids are getting high off their urine) Cartman has to hide his cat in the attic. Then he ends up hiding one cat he finds in his backyard. Though each time he says no more, he finds himself harboring every cat in the town, in a blatant holocaust reference. When it's all over and Kyle asks Cartman if he sees in similarities between this and some other part of history, Cartman is clueless.
Cartman has shown genuine love for his mother and gets very upset when Stan's grandfather disrespects her.
In The Simpsons, Mr. Burns has one when he decides to take care of The Simpsons' puppies. Admittedly, he was first planning to make them into a coat, but he did decide to spare them later on.
In the flashback episode "I Married Marge", Homer leaves Marge (without saying where he's going) to get a real job so he can care for her and their unborn baby Bart. Seeing how despondent Marge is without Homer, Selma tells her where he is, despite the fact that she really doesn't like Homer.
Cotton from King of the Hill hates most things and most people for no reason. But most scenes featuring him and Bobby have him showing his own brand of love.
His greatest Pet the Dog moment occurs when he took the blame for Bobby for the church fire after Bobby got stomach problems from eating the entire batch of lutefisk. Even though Cotton chastised him and called him "Stinky", he nonetheless took the blame.
Heck, he even gets a few moments with of all people, Peggy, his Sit Com Arch Nemesis. In the episode where she learns to walk again. Cotton immediately begins rallying Peggy in his own twisted way. It seems a bit like an Out-of-Character Moment for him, but then Hank points out that Cotton also had a traumatizing injury like Peggy and, like him, had to learn to walk again, when the doctors said that he never would.
Vicky's pets, particularly her dog Doidle, are the only beings she treats with any respect. But a more amazing example about Vicky comes in the storybook In a Tizzy over Turkey!: Her parents and Tootie (who she treats no different than the kids she babysits) go out to get some cranberry sauce, but their car breaks down, and Vicky is actually sad that they're gonna miss their Thanksgiving dinner! Yep, even Timmy feels sorry for her when he hears that...
Used with little subtlety in How the Grinch Stole Christmas!, when Cindy Lou Who wakes up and sees him looting the family's presents. He could have just tied her up and gagged her, but instead he tells her a comforting fib, gets her a glass of water, and sends her back to bed, foreshadowing his Heel-Face Turn.
This is Played for Laughs in the live action movie, when the Grinch saves her from a mail machine. She sees it as proof that he's a good person, and he gets pissed and wraps her up in wrapping paper (though she is still unharmed, and her parents assume that she had trouble wrapping some gifts).
Heloise on Jimmy Two-Shoes has had few. A lot have to do with her Morality Pet Jimmy. She had a literal example with Cerbee, and again with a poodle rat in another episode.
Kim Possible. Shego's been known to do this... in her scene with Senor Senior Junior she's shown to be genuinely caring.
Recess: Miss Finster is prone to this, usually with Spinelli. She also pulls this trope at the end of Recess: School's Out, after finding out that Miss Grotke's a martial arts expert and finds a newfound respect for her. This is especially heartwarming when in previous seasons, Miss Finster's shown not to like her too much.
Almost every character in Archer is an unsympathetic/borderline sociopathicJerk Ass, but they've each gotten at least one moment each.
Archer insists on stopping and getting a stuffed animal for Babu the ocelot, to make up for the spartan conditions of Cheryl's care.
Malory cares for Archer when he is shot six times in the chest. It was Malory who shot him, but Malory being Malory, it still counts. Malory also bribed Mexican officials to save Woodhouse after he shot a woman in Mexico in a heroine-fuled bar bet.
Lana has a bizarre one when she agrees to have pity sex with Pam.
In the Transformers Prime episode "Triage," Soundwave, so far known to just about everybody to be silent, mysterious, and downright terrifying, leaves his battle against Wheeljack in order to go rescue Laserbeak, after receiving an S.O.S. from the drone. May count as a double example because there was no reason whatsoever that he couldn't go ahead and eliminate Wheeljack, who had been disabled through painful audio waves, before leaving.
Not to mention in season 1 he spares the kids, even when Miko unintentionally gives him a fire axe.
Sandi is probably the closest Daria has to an antagonist, aside from Ms. Li. There are a few episodes where Sandi appears to hold genuine disdain for Quinn (and in one case, even just sits back and smiles after sabotaging Quinn's play.) However, at the same time, you can view her Character Development as she starts to mature. It's probably most prevalent in the episode where she gains weight, and even though she manipulates Quinn into taking a sabbatical from the Fashion Club, is moved to tears when Quinn instead respects her wishes and uses the time to help Sandi get back into shape and out of her depression. Another episode, where a stalker is giving Quinn free goods in the hotel, Sandi is the only one who smells a rat. It's easy to interpret this as her trying to deny Quinn from having a cute boyfriend, but it's also just as easy to interpret this as genuine concern for Quinn.
Even earlier than that, in the paintball episode, Sandi chews the Fashion Club out for not wearing the safety goggles.
SugaMama is also one of the few people they genuinely respect.
Horrid Henry. Henry is an Unsympathetic Comedy Protagonist who is frequently an asshole to his little brother Perfect Peter as well as his classmate Moody Margaret and cousin Stuck-Up Steve. (...then again, Margaret and Steve deserve it.) However, he does show Big Brother Instinct towards Peter a few times, and during the sleepover episode, decides to have fun with Peter and his friends, instead of at their expense.
As bad of a parent as he is to his son PJ, in the episode "Puppy Love," he did many nice things for him without an ulterior motive such as giving him dating advice, renting a limousine and offering to be the chauffeur, taking some (of Peg's) earrings for him to give to his date, and preventing Max from stealing his date... too bad all of those things made PJ's life harder, but in contrast to how their relationship usually plays out, it was completely by accident.
A straighter example happened in "Tee for Two" when Pete gave up the trophy he finally won after resenting the mini-golf course for years because he never won it to a random little boy at the end. Peg has to give him a big kiss for this one.
In the Christmas Episode "I Heard the Barks on Christmas Eve" of Pound Puppies (2010), reluctant dog catcher Lenard McLeish, who allegedly didn't like dogs, finds an equally hard luck dog named Ralph to take in to his home and heart.
In Young Justice, Black Manta may be a member of The Light and clearly evil, but he cares deeply for his son, Aqualad, to the point of going Papa Wolf on anyone who might hurt him.
Zigzagged with Sportsmaster. Sure, he'll blackmail and emotionally abuse his daughters, but he swears revenge against Black Manta when Manta's son kills his daughter, Artemis... but only because he did it without his permission. He wants to kill Manta to preserve his reputation, because he'll look like a cheap punk if he lets it go or takes a payoff. However, when he finds out Artemis faked her death in order to screw over Manta and the Light — the employers Sporty broke with in order to pursue killing Manta — he's perfectly fine with allowing the Light to believe he lost the fight against Manta and even covers Artemis' tracks as a favor.
Several characters in Moral Orel do this later on, particularly Coach Stopframe in the finale. Reverend Putty also has moments like this throughout the show.
Ratty from Mr. Bogus, of all people, actually shows shades of this in the first act of the episode "Babysitting Bogus", as while acting as MC for the wrestling match between Bogus and the baby, he acts concerned when he sees Bogus getting creamed by the baby, and he elatedly congratulates Bogus for hypnotizing the baby into taking a nap.
The Adventures of Sonic the Hedgehog has Doctor Robotnik and "Fuzzy-Wuzzy", his old favorite toy and only real friend. Yes, Fuzzy-Wuzzy is a robot bear that can turn from a creepy teddy-bear into a horrifically real two-headedfour-armed grizzly, but Robotnik still cares for him deeply. When Sonic disables Fuzzy-Wuzzy by tying him to an electric fence, Robotnik is horrified at the fact his friend is being hurt and falls on his hands and knees before Sonic, pleading with the hedgehog to save Fuzzy-Wuzzy and promising to be good if Sonic will.
Mumm-Ra from Thundercats is an evil Big Bad who'd like nothing more than to eliminate the Thundercats and rule Third Earth unhindered...but he loves his pet Ma-Mutt, to the point where he actually apologizes to him in the episode "Ma-Mutt's Confusion".
Plankton gets one in the episode "Plankton's Pet". He's genuinely nice to his new pet amoeba Spot - when Spot eats the Krabby Patty he helped steal, Plankton's only response is to calmly tie him up for a few minutes as punishment - and when Spot runs away, he willingly works with Spongebob to find his pet and doesn't even TRY to steal another Patty.