In Metal Gear Solid, a female villain pets a dog to prove her not-all-bad-ness. One of the characters remarks that her love of dogs must mean she's good inside, prompting the main character to rant about how her love of dogs proves nothing. While it might seem like a subversion at the time, as we proceed it turns out that the villain is not a creepy stalkerish murderer, but a lonely dog lover who only wants to be loved. Then Snake kills her.
Snake's love of animals probably counts too, because it's the first suggestion we get that he's anything other than an action hero with no inner life.
If anything Snake's dismissal of Otacon's defense of Wolf on this basis is deeply ironic and not a little tragic - he loves dogs too, but he believes himself to be an intrinsically worthless human being outside of the battlefield. Snake's self-loathing becomes more apparent by MGS 4, until Big Boss reappears, more-or-less apologizes to Snake for how fucked up his life was, and then tells Snake to live out the short remainder of his life in peace and happiness.
From Sons Of Liberty Fortune blasts apart a squad of Navy Seals for not being able to shoot her and then apologises to the dead seagulls that got hit by their bullets.
"I'm so sorry my beauties. I'll see you again someday"
In Warcraft III: The Frozen Throne, Illidan Stormrage is a power-hungry, demon-night elf hybrid. Still, he goes out of his way to help save Tyrande, his sister-in-law, for whom he harbors an unrequited love.
Seeing how His brother acts towards him every time he gives him a chance to, from the war of the ancients and forwards, one can argue that he's actively been working to turn him into a villain in order to secure Tyrande for himself, which in some ways would make a lot of the good things he does fall into this trope's territory.
In World of Warcraft, Kel'Thuzad is an undead lich who serves as The Dragon to Arthas Menethil, the Lich King. However players can confront a kitten named Mr. Bigglesworth in his lair. If killed his reaction seems to be sadness and vengeful hatred towards those heartless loot-seekers that just killed his kitty.
King Varian Wrynn, who is considered a racist jackass by some, gets one when he allows an enemy general to pass through Alliance lines unmolested so that he could retrieve the body of his slain son.
Garrosh Hellscream, his is clear counterpart among the Horde, got one as well when he executed a warlord for attacking innocents and showed respect for the wisdom of a still-grieving Tauren chieftain.
Shadow Hearts: Covenant has a Giant Mook named Lenny, who is a recurring foe on the first disc. On the second disc, however, one Sidequest reveals that he spends considerable amounts of time petting the dog. Among other things: he saved an old woman from muggers, he sent one mook with an ailing mother to report to their boss and thus saved him from certain death on the next mission, and he made a poor thief self-sufficient by teaching him math (which helped him get a job).
And in the sequel, when Johnny gave him a glass of water a few years before the game, he vowed to serve him for life, serving as a Battle Butler and being the muscle behind his top-tier Tool attack.
Sonic Adventure 2: During the game's final story, Eggman sets aside his rivalry with Sonic and company to stop the ARK from crashing into the earth. While the credits roll, we see Eggman having a friendly conversation with Tails about how he used to idolize his grandfather (the man responsible for almost destroying the world this time).
God of War: Chains of Olympus seems to have a number of cinematics showing tender moments between Kratos and his family, before you-know-what happens. The ultimate peak of this, Kratos reuniting with his daughter after renouncing his violent past and powers, is followed by a heartbreaking Shoo the Dog moment, in which he has to shove his daughter away (in one of the series' trademark button mashing minigames no less) in order to save the world. It goes a long way to establish just why Kratos is so goddamn angry in the later games.
Soul Nomad & the World Eaters: At the end of the Normal Path, Gig admits his regret over everything Drazil made him do, taking responsibility since he still enjoyed what he did even though his personality was changed.
In the Demon Path Dio is risking his life to save his queen and eventually has a full blown Heel-Face Turn.
Subverted in the Demon Path where Revya saves the life of a angel just so that s/he could kill her friend right in front of her. This behavior is also mocked when Lobo is revealed to be a traitor in the Demon Path, specifically if you choose to say that you trust Lobo, his Freudian Excuse kicks into play and he leaves you, claiming that people who trust each other are fools. Gig mocks him for it.
Phantom Hourglass, Linebeck spends the entire game as a gutless coward who has to be bribed by the Ocean King to convince him to help out at all. At the very end of the game, he sees that Link lost his sword and is being attacked by Bellum and promptly stabs the demon to give Link a chance to fight back. The poor guy is then possessed for his efforts.
At the end of Wind Waker, Ganondorf knocks out Link and steals the Triforce of Courage, but promises not to kill him or Zelda. Unfortunately, this goes out the window a second later when he loses the chance to rule Hyrule and goes rather crazy, determined to drown them all.
Subverted and used quite literally, after you rangle the goats in Legend of Zelda: Twilight Princess, you are able to stop, drop whatever you're doing and pet them. Whoopee.
Sagat allowed both his former student Adon, who coveted his title, and Joke Character Dan, whose father he killed in a fight, defeat him to gain either the title or closure they sought. The second instance was the first step in his Heel-Face Turn, as he saw how much obsession with revenge ruined Dan's life (at the very least, it caused Gouken to turn him away partway through training, resulting in his Joke Character style), and he realized his obsession with Ryu was doing the same to him.
Balrog, of all people, gets one of these in Street Fighter IV. Bison's plans have, apparently, gone to Hell, and Balrog is stomping around the ruined base looking for some treasure to loot before the whole place blows up. He runs into a scared little girl instead, and opts to carry her out. He only decided to save her after he discovered she had some sort of special powers, so his motives might not be as altruistic as they seem...
In a very literal example from the same game, the Mayor of Iselia, who was firmly established as a racistJerk Ass in the previous game, can be found petting his dog.
In the original Tales of Symphonia, Yuan gets one of these in a sidequest as well. After spending the entire game as a cold, impatient, manipulative bastard who appears not to care about even the Heroic Sacrifice of his closest subordinate, you follow him across both worlds on a sidequest where he's searching for something that he sharply refuses to explain. Turns out it was his engagement ring to Martel, and when he finds out that Lloyd was the one who picked it up, he's willing to literally beg for its return.
Jade: That's what I would say if I was an emperor, with a country and people to look after. As your friend...I feel compelled to stop you.
Luke: I didn't realize you thought of me as a friend.
Jade: Oh? Of course not. I can be a terribly cold person...I'm sorry.
In MOTHER 3, Fassad is shown as being down right evil: torturing monkeys, and corrupting innocent civilizations, but after he is defeated, the player meets his pet mouse who is eagerly awaiting his beloved master's return.
Minor example: In Persona 4, there's a snippet of dialogue from a Yasogami student that hints that Sadist Teacher Kinshiro Morooka can have some pleasant moments, as the student said that she got some candy from him. He's also in the habit of offering serious career advice to his students on the sly. However he's always a jerk towards the protagonist and his friends so they never actually see this aspect of him.
Save the truly villainous ones, the normally antagonistic rival prosecutors in Ace Attorney games each have their own Pet the Dog moment to prove they're not as mean as their courtroom abuse of Phoenix would have you think.
In "Bridge to the Turnabout", the smug Godot shows a soft spot for children when he comforts a distraught Pearl by giving her his last cup of coffee, and sweetens it for her.
The flashback to Mia's first case shows that the arrogant Diego Armando still showed up to assist a rookie like Mia, when Grossberg overslept.
Word of God reports that Miles Edgeworth has a literal dog, named Pess, whose death would probably completely shatter him.
Franziska has her soft spots, particularly towards young children and the hapless Adrian Andrews. Even if she previously manipulated Andrews' codependency issues for court purposes.
In the non-prosecutor department, Matt Engarde has a cat named Shoe who he asks you to feed.
Subverted by Manfred von Karma taking a young Miles Edgeworth in, after Edgeworth's father died. Teaching the kid everything he knew and training him for his career sounds like a kind thing to do for the son of von Karma's rival, but actually, von Karma just taught Edgeworth to be as ruthless and amoral as he is. He also did it with the ultimate intentions of framing Edgeworth for murder and getting a very strung out revenge on Gregory Edgeworth.
A subtle variation of this may have shown up in Pokémon's fourth generation games: Cyrus, the nihilistic and emotionally disturbed Big Bad who proudly claims he only uses Pokémon for their power, has a Golbat that in his final battle has turned into a Crobat. Golbat only evolves into Crobat when it has developed a particularly strong bond of friendship with its Trainer.
A far less subtle case is where Cyrus, after the hero battles through his mooks and defeats him in battle, praises the hero's courage, gives him/her a Master Ball as a reward, and tells him/her where to go to save the Spirit Pokémon. In Diamond and Pearl, this ends up ruining his plan, but in Platinum, he's more prepared.
Archie and Maxie in the Hoenn games also use Crobat, though they are Well-Intentioned Environmentalists so it's not a far jump for them to be responsible Pokemon Trainers.
Skies of Arcadia: Mercenary helmsman Lawrence borders on being a Jerk Ass most of the time, but when he's not on duty he chooses to hang out with Pow, so he can't be all bad. Also, when the Crescent Island base is destroyed, he is seen clumsily trying to corral the escaped chickens.
In Project Origin, one of the intelligence files reveals that the music box that appears early on in the game in Genevive Aristide's apartment (and is the source of the recurring theme music throughout the game) originally belonged to Alma, and that Aristide had it brought to her home, so she could listen to it and remind herself of how guilty she is herself.
Given Aristide's greedy, self-justifying behavior and comments in both Project Origin and the supplemental promotional materials, the idea of Aristide feeling any guilt over Armacham's treatment of Alma seems highly unlikely. Maybe Aristide just likes the music box's tune.
Alma herself has a few Pet the Dog moments toward both the Point Man and Becket, like when she kills a group of Replicas that have the Point Man pinned down in Extraction Point, or when she kills an Abomination that is directing Replica soldiers against Becket, or kills ATC troops in Becket's path in Wade Elementary.
Fable II: You can play as evil as you want, but your faithful dog still loves you.
In Dynasty Warriors: Empires the ending consists of a 'clip show' with various officers of your faction in "Romance of the Three Kingdoms outakes". One clip shows one of your officers leaping in front of a runaway carriage to save a small lapdog, then with their most heroic and staunch Chinese Warlord face, they nod approvingly over the tail-wagging little thing. Especially funny when a real jerkass officer like Lu Bu does it. Downright hysterical if that officer happens to be the Emperor of China at the moment.
An Ace Combat 4: Shattered Skies cutscene shows the enemy ace Yellow 13 holding and petting a small dog. He also saves the narrator and the barkeeper's daughter from getting caught by military policemen after the latter is seen planting explosives.
Subverted in Hitman: Blood Money, where throughout the game, you see the cold blooded killer keeps a pet canary. However, the moment the bird starts chirping at an inopportune time: * crunch* .
Also subverted in Contracts, where 47 has the option of petting the dog in order to advance his agenda: for example, he can offer to take the place of a tired bartender- so he can poison a customer's drinks.
Lord Wily of the Mega Man Battle Network series has paid for the medical treatment of Joe Mach's daughter, and he also temporarily abandoned his quest for revenge on society to take care of Baryl for a friend. He also gets a Crowning Moment Of Awesome when he walks into an exploding volcano to rescue his own son Regal and give him a second chance to be an upright human being courtesy of Laser-Guided Amnesia mixed with a rather amazing Reset Button.
The one from the classic series gets a few too; in Mega Man 10, he turned out to be the villain again, but, when he got a fever from Roboenza, he was put into the hospital, he escapes soon afterward, but not before leaving enough Robonenza cure capsules to cure a population, and if it's not enough, they could still examine it and determine the cure, Wily may be a villain who wants to take over the world, but he's not a heartless monster.
A cinematic in Samurai Warriors: Empires has Nobunaga trying to cheer up Nene when she's upset by her husband's philandering. (This one happens to be Truth in Television, quoted straight from a letter Nobunaga wrote to Nene.)
In the Sengoku ending of Warriors Orochi, XiaoQiao gets upset when the three main characters (Nobunaga, Uesugi Kenshin, and Takeda Shingen) start trading not-so-veiled threats at each other, so Nobunaga chuckles and pats her on the head. (Its All There In The Manual - Xiao Qiao reminds him of his sister Oichi.)
In Samurai Warriors 2, this gets raised to Ho Yay levels when he sheds a tear at Mitsuhide's death in his ending.
In Continuum Shift he gets another. When he meets Tsubaki Yayoi, instead of brushing her off, as he does most people, he sits down and asks her to 'listen to an old man's tale'. He tells her of a story of a woman he loved, but who tragicly died. He was referring to Tsubaki herself, as Hakumen is really Jin Kisaragi from the previous time loop. Then once he figures out Hazama's plans for Tsubaki he finds this loop's Jin and convinces him to go save her, not wanting her to die in this loop too.
Alternatively in his Bad Ending upon realizing the plan Hakumen goes to fight Hazama himself only to find that's she's already blind while Hazama beats her while she's down and insults her at which point Hakumen completely loses it.
Also, in the first game, Ranga the Bloodedge is given two options after defeating Arakune in his story mode. Option one is to just leave and let Litchi greave over him. Option two is to stay behind and finish the job. If you choose this option, Ragna stays and argues with Litchi over why she should let him kill Arakune. Eventually, he leaves her and grumbles something along the lines of "If you wanna save him, go ahead. It's none of my business." But, as he leaves, he also quietly whispers "Good luck."
He gets another one with Taokaka. After fighting him in her story mode, Ragna offers her some of his food.
In Continuum Shift, Jin Kisaragi is a complete asshole who throws death threats to anyone who gets in his way. However:
Although to a much lesser extent than Tsubaki, he's also quite friendly to Makoto, if a little snarky. He seems to genuinely care for her well-being, saving her life when Hazama attempts to "discipline" her (read: he's trying to off her because She Knows Too Much).
He also seems genuinely sorry for the female officer he knocks out to escape the NOL ship at the start of his story.
In the Drama CD The Wheel of Fortune. It was shown that when they were kids, he is rather affectionate to Saya before she became sickly. The reason for Jin's hatred towards Saya and why she suddenly became ill is as of now unknown.
The protagonist of the remake of The Bard's Tale is an Anti-HeroJerk Ass more interested in, as the game states, "coin and cleavage" than saving the world. He is a compulsive liar and cheat, swindling his way through life and seducing his way through women. However, not only does he pick up a dog companion early in the game, but he sheds a genuine tear and vows revenge when the dog is killed by a monstrous minion of the apparent Big Bad.
In Dragon Age: Origins, Loghain can get one if you have him in the party with your dog. It turns out, that part of the reason he hates the Orleasians so much is because they killed his dog.
In Mario & Luigi: Bowser's Inside Story, Bowser, when facing his troops who went AWOL, decided not to scold or punish them instead told them to continue what they were doing and that they needn't worry of the situation.
In Valkyrie Profile, the PC acts as a Psychopomp, recruiting Einheriar from the 'worthy dead', and sending the rest to Hel. One of your recruitments features a low-down thug named Badrach, who's popped up in the stories of several other characters before - including participating in the kidnapping and transport of a princess, which led to her death. When his deeds finally catches up with him, he drags himself home to his worn-down little house, and his sharp-tongued wife, bleeding all the way before collapsing on the doorstep... and in the afterlife, he finds Lenneth Valkyrie waiting for him, only too eager to send him hurtling down into Hel - but she gives him a chance: Did he ever do ANYTHING worthy? A single good deed? He first tries to lie, but he cannot - instead, he merely spouts a string of crimes, from mugging and burglary to outright murder. But finally, he does recall a single redeeming act - one time, he was running security for slavers, and one slave, a little girl, took a shine to him. When the slavers' pay didn't measure up to his expectations, he ditched them and took the girl out of spite, bringing her to...an abandoned church. Probably better than staying with the slavers, though.
A bit interesting if you look closer, its implied the girl he saved was lucien/rucio's sister that was sold off in the prologue.
In The Incredible Hulk: Ultimate Destruction you generally run around doing whatever you want, and that usually involves the killing of many, many, many innocent people. But if you so choose to grab a person you have an option besides throwing them into the distance: Putting them down gently and patting them on the head.
Subverted by a literal case in Fallout: New Vegas - the Legionary Antony displays more regard for the dogs under his charge than he does for people. He offers his aging favorite to be killed in the arena for the possibility of giving her immortality as the brain of a cyber-dog, and he gives the other dogs a teddy bear to play with - which he took from a child slave.
Played straight in the ending if Caesar's Legion wins and Caesar himself is still alive. One of the only non-evil things he does is let the humanitarian organization Followers of the Apocalypse leave Vegas peacefully because he himself was raised by the Followers.
In one notable scene, the NCR are handing out supplies to the NCR refugees in Freeside. If you pose as a refugee for a quest, you get a dialogue option where you mention having a local friend who needs food. The NCR officer mentions being under strict orders that they cannot offer food for locals. Right before handing you another food package to take back to him.
If you get a relationship value of Accepted with the NCR, a Ranger will appear and meet you out in the wastes. He'll give you a radio and explain that you can call for NCR support should you need it.
Even you can get a few. You will be very likely playing as some form of Anti-Hero, anyway. For example, with a high Charisma score, you can play with the Boomer children and give them toys. Regardless of your alignment.
Revealed near the very end of Dead Space 2. Director Tiedemann, who seemed throughout the game to be a cold, ruthless Corrupt Corporate Executive, is in fact shown via three audio logs to have had the best interests of humanity in his heart. He went along with the Marker project because humanity was slowly dying out and he thought that this was their best hope for salvation, and when the outbreak occurred he blatantly disregarded the protocols set in place by the shadowy figures in charge and called for a station wide evacuation, doing his best to save as many citizens as possible from the necromorphs.
Subverted in the non-canonical ending of Tekken 5. Kazuya actually paid respect to his grandpa Jinpachi before fighting him by giving him a respectful bow. After beating him, he even cradled him on his hand while remininscing his past with his grandpa, when he was an innocent boy... cue Kazuya getting his Evil Eyes activated, killed Jinpachi with his own hand and cue another Evil Laugh... He got you again, didn't he?
Gogandantess from Onimusha 2: Samurai's Destiny is a highly arrogant Genma who is the self-proclaimed "greatest swordsman of all demons". Although he isn't nearly as evil as the other Genma shown in this series - in fact he is very honorable and chivalrous - he's still definitely a bad guy. So, it comes as a surprise to Jubei (and the players) when, just as it looks as though Oyu is going to plummet to a firey death, Gogandantess leaps in and saves her at the last second.
Depending on your playthrough of Mass Effect, Commander Shepard has his moments. Most notably if s/he's usually renegade and starts abusing NPCs outside his/her crew but takes a moment to console his/her squad with any problems they might have. This can be played fully straight if s/he's constantly renegade all the time in the sequel but takes the paragon route on the crew's loyalty missions.
Zaeed in the Citadel DLC gets hooked on a claw vending machine game while trying to win a toy for a child. Bear in mind that Zaeed is pretty much a Psycho for Hire and regularly discusses, in a very casual way, how [thing] wiped out half his squad once.
A Renegade Colonist Shepard gets one in the I remember me mission, when dealing with a badly traumatized girl taken as a slave in the same raid Shepard narrowly avoided. Renegade Shepard encourages the girl to be strong and tells her that she is strong enough to face what happened.
Kitsune, the fourth Lord of Chaos in AdventureQuest Worlds, is extremely fond of all of his fellow Yokai. When Emperor Daisho started inviting foreigners from outside Yokai Island to the island itself, Kitsune became furious and didn't share the same sentiment with Daisho, vowing to do everything he could to return the island to its former secluded sanctuary - which is how Drakath made him the fourth Chaos Lord. Kitsune became a Magnificent Bastard as soon as Drakath convinced him to use the Hanzamune Dragon Koi Blade to free the O-dokuro from its prison in the rift of time.
Zahart was extremely fond of Tibicenas, the eighth Lord of Chaos, whom he got the ability to summon and command after Drakath gave him a chaorrupted magic ring. He was so fond of Tibicenas that he wanted to use him to rule the Sandsea for all eternity after paying off his debt to Drakath by using the red diamond found by his slaves to animate the Chaos Sphinx. Unfortunately for him, Tibicenas has plans much worse than he himself had originally planned.
And in the Doomwood saga, Drakath, being the Affably Evil guy he is, has landed himself in this spot since he kindly retreieves Vordred's helmet and returns it to Sally.
Yomielpossesses people to force them to commit crimes, cuts a deal with a foreign nation who will almost certainly use what he offers them to attack other countries, and manipulates poor Kamila into killing her own mother, albeit indirectly. Towards the end of the game, he saves Lynne and Kamila from drowning by breaking open the submarine door that's stuck and manipulating junk to make an arm to pull them out.
We also get one from Dandy, who is very polite and kind to Kamila, even when he kidnaps her, giving her a book and juice, finding it disturbing that he and his associate were asked to hold Kamila captive in the remains of her former home, and crying over Kamila's fate in the timeline when she was crushed to death.
Travis Touchdown of No More Heroes, a perverted, Blood KnightOtaku, has a thing for cats. He owns a Scottish Fold, Jeane, which he can interact with in both games and one of the jobs in the first game has him finding runaway cats.
Yeager of Tales of Vesperia was portrayed as one of the Big Bad's servants, and was considered to be evil and manipulative. However, there are two girls who're helping him, and during his final battle, explicitly ordered them to not join in the fight between him and the heroes, heavily implying that he wanted to die. If you do a big of digging, you find that Gauche and Droite were actually from an orphanage that Yeager funded, and pledged their lives to help him.
In Kingdom Hearts: Birth by Sleep, after Splitting Ventus' heart in half and creating Vanitas, which nearly killed him, Master Xehanort took him to his homeland, the Destiny Isles, so he could spend his last moments in a peaceful world. Then cruelly subverted when Ven connects to Sora's heart and recovers, and Xehanort makes him suffer much, much more.
King Foltest from the The Witcher games is generally described as "The arrogant, sister-humping warmonger", a completely justified characterisation. However, he is A Father to His Men, and recognises and remembers the name of a private from a battle over four years earlier. Also, when interacting with his children, he turns into a complete creampuff.
After a Space Route scenario in Shin Super Robot Wars, Laodecia finds a capsule with a weakened Earthling floating inside. She manages to say that her name is Fuala before losing consciousness, and Laodecia orders her tended to. This act apparently caused Fuala to become loyal to the Balmarians' cause.
The Boss in Saints Row 2 comes across as a sociopath who revels in the evil s/he does. In Saints Row: The Third s/he mellows out considerably, particularly in regards to the other Saints. The god ending and DLC have this further, with Boss positively nuzzling Jenny to the point she becomes a Promoted Fangirl by standing up for herself and killing her Jerk Ass director, knowing Boss will have her back.
Troy Bradshaw as well...after becoming police chief he keeps Boss on life support and gets Gat protection in prison as a way of making up for being an undercover cop with the Saints.
Killbane get one in Saints Row the Third when he lets Matt Miller leave the Syndicate with no strings attached. He even offers himself as a job reference! This is further highlighted by Matt clearly antsy and fearing Resignations Not Accepted the entire time he's walking off, especially since Killbane broke the neck of the last person who said they were getting out.
In Robopon, at the beginning of Robopon 2, Dr. Zeke finds Cody washed up on the beach and saves him, taking him to his house until he wakes up. Unlike his brother in the previous game and his father, he seems to be an Affably Evil kinda guy.
Team Fortress 2: In the supplemental comics, the otherwise morally questionable mercenaries draw the line when children are involved, and always act kindly towards them. (Even if, in the case of BLU Spy, "acting kindly" means teaching a little kid how to use an icicle as a weapon so he doesn't get kidnapped.)