Part of the reason he resists allowing Phoenix to take his case in Turnabout Goodbyes despite having been accused of murder is because it would potentially ruin Phoenix's career if Phoenix lost. He also apologizes for telling Phoenix that he's a horrible defense attorney, stating that he'd only been trying to make Phoenix go away, and he hadn't really meant it.
He helped Phoenix stall for time in Case 2-4 of Justice for All in order to give Gumshoe time to find Maya, who had been kidnapped by an assassin, despite not even knowing about it. All he knew was that Phoenix was freaking out about something, so he just jumped in to help draw out the trial and requested a ten-minute recess so he could ask Phoenix what was going on.
In Trials and Tribulations, he charters a private jet and flies back from overseas the instant he hears that Phoenix might be dying in Case 3-5. (He's mostly fine, as it turns out, but since this was after he had plunged off a burning bridge into a rapidly-flowing river famous for killing many people in the middle of winter, the concern was justified. Directly afterwards, he risks his career for Phoenix's sake by pretending to be a defense attorney in order to defend Iris on the first day of her trial, as Phoenix had not yet been released from the hospital.
Franziska von Karma in the second game. She has a nasty temper and a tendency to attack people with a whip when she doesn't get her way. However she is kind to Adrian Andrews and she cried when Edgeworth showed brotherly affection for her. Also, in the third game, she got upset when Pearl yelled at her.
Diego Armando from Trials and Tribulations is the typical "romance novel" type Jerk with a Heart of Gold. He comes off as cocky and patronising towards women and he's very self assured. However he's also dedicated to catching criminals and shows care for Mia.
Maximillian Galactica from Justice for All comes off as arrogant and self-conceited, but does so with the hopes that it will get his circus mates to strive to become better and follow in his example.
Shi-Long Lang from Ace Attorney Investigations appears at first to be a total jerk who irrationally hates prosecutors, but near the end he helps Edgeworth take down the real mastermind behind a smuggling ring, as well as taking a bullet for his traitorous assistant.
The "grumpy" male animals, especially in the later games. Though they are self-admitted curmudgeons, they warm up to you fairly quickly, and even though they tease you, they're very glad of your friendship. They even cry with joy if you show up at their birthday parties!
Mr. Resetti tends to rage at players who constantly reset the game, to the point where he tricks them into thinking he erased their games, but at heart he's just advocating them to play the games like they're living their lives, as Save Scumming isn't the way the game is meant to be played. His older brother Don at one point shows up in his place to appologize for his outbursts being a blight in their family's reputation. Notably, Resetti himself is self-restrained the first time you reset the game, warning you not to get too intimidated by his harshness if you keep resetting the game.
Kazooie, the loudmouthed bird from Banjo-Kazooie. She doesn't show it much, but she does care about Banjo deep down. When she and Banjo get separated in the beginning of Grunty's Revenge, she's happy as a clam to see him again. She also occasionally lets slip her concern for other characters; there is a scene in Banjo-Tooie where, during the sidequest to save the frozen baby aliens, Kazooie goes "Aww..." out of pity, before catching herself and pretending she doesn't actually care.
Kalas from Baten Kaitos: Eternal Wings and the Lost Ocean. He's a cynical jerk and an Anti-Hero, but if you hurt someone he loves, he'll chase you to the ends of the sky.
Luka is a Handsome Lech and a huge pervert most of the time, but he does have a heart and cares for his friends.
Enzo is an overweight loudmouth with a foul mouth and short fuse, but as Bayonetta herself notes in the sequel, he's a surprising family man.
Loki. He's a Bratty Half-Pint who uses enough foul language to make a sailor blush, but at the end of the day, he does care about Bayonetta and is quite willing to help her out... though he understandably draws the line at marching right into the gates of Hell.
Augustus Sinclair in BioShock 2. A self-interested capitalist whose goal is to use Subject Delta to steal the technology of Rapture for profit, he nonetheless does go to great lengths to help Delta in his quest rather than leaving him to die and encourages him to show mercy. In the end, when Sofia Lamb turns him into a Brainwashed and Crazy Alpha-series Daddy, he encourages Delta to put him down and helps him with the last of his free will.
Ragna the Bloodedge from BlazBlue. For someone who is feared as the Grim Reaper, curses and trash talks a lot, just as long as you're not after his head, he is usually a nice man and an example of Dark Is Not Evil. This is lampshaded by Litchi when he decided to spare Arakune after she pleaded him to (he is also against beating up women for no reason). This is very contrasting with his complete Jerkass of a brother, Jin.
Also, to a lesser extent (on the "Jerk" front at least) is Bang Shishigami. He can be rather thoughtless, will beat up anyone trying to talk to Litchi (even if she's the one who initiates the conversation), and, in Noel's story mode, beats her up and walks away laughing while she breaks down and cries. That said, he's also a very well-meaning individual who cares much more for the well-being of his village and those who follow him than his own personal safety, will never back down from helping those in need (though he may be incompetent at it), is strictly adherent to his code of no killing, and, in each character's respective Joke Ending, takes Taokaka and Carl under his wing to train them.
Even Jin gets in on this, in the sequel. Jin was revealed to have the great deal of his Jerkass attitude from being Brainwashed and Crazy by his Evil Weapon Yukianesa, and ends up being closer to this trope to anything else. By this point, he's closer to his older self, Hakumen, than how he was in the first game.
Rachel Alucard also qualifies. She's a jerk to everyone but especially to Ragna, and she can get downright nasty when she feels she's not being treated with the proper respect. At the same time, she's willing to go out of her way to help Ragna, even if it means upsetting her superiors.
Bullet of Chronophantasma is abrasive, anti-social, ill-tempered and has a tendency to hold grudges, but she's not a villain. Only Bang gets to see the "Heart of Gold" part, though.
Kagura of the same game is a colossal pervert who gets easily distracted by any woman he comes across, particularly Makoto. But he's one of the coolest guys to hang out with and despite his flirtatious ways, he values women as people. On that note, harming a woman in his presence is ill-advised.
Before Ragna, there was his spiritual predecessor, Sol Badguy. Sol swears a lot, trash talks a lot, maintains an edgy, standoff-ish approach to strangers, and his idea of helping someone collect themselves is kicking them full-bore in the face. However, he has nothing but altruistic goals, and what few friends he does have, he's rather decent to. He also seems to have a soft spot for young girls: in Midnight Carnival, he helps calm down Dizzy after she loses control of her Gear powers, and in Xrd, he's rather mean and distrustful to Elphelt through the story, but when she's being brainwashed and robbed of her will, Sol was the most passionate of all the good guys in trying to save her.
Jimmy, the main character of Bully. In the opening cut scene Jimmy appears disrespectful to his mother and new step father and starts off quite unsociable. However he does mention that "I only give people what they have coming to them." He proves to be as good as his word, as his early missions involve protecting the Nerds from the Bullies. He goes out of his way to help the ugliest and least popular girls get their stolen items back and told the biggest kid in the school that "There are a lot of kids at this school who need a beating, and you're picking on the few who don't! So I want you to leave me and him (Petey) alone!"
Frog from Chrono Trigger, but only in the Japanese version - his dialogue was changed in the English translation such that he was chivalrous and polite (and with pseudo-Shakespearean syntax in the SNES version) instead of abrasive and aloof.
Nero from Devil May Cry 4. Prone to badmouthing the church, listening to loud metal in said church, not allowing anyone to work on his team (which consists of himself), back talking to Kyrie's brother, taking great pleasure in insulting basically the gods of Hell to their faces, and anything else that happens to come his way, including Dante. But in that titular scene in the prologue, you see that one smile he gives to Kyrie when she's on stage that makes women everywhere pine for such a sweet guy.
The scene at the end of the credits where Kyrie is looking all dramatic and thoughtful and Nero swaggers up behind her. She takes his hand - his demon hand - and gives it a little squeeze...which he returns. Then he promptly goes all bashful and can't look at her, with a dorky little smile on his face. Just don't screw with her. Ever.
Dante himself counts. He's abrasive as all hell at first (especially in 3), and initially acts like a Handsome Lech towards Lady, but it's implied he does a lot of pro bono jobs when people actually can't afford his services, and comes around to saving the day simply because it's the right thing to do. He's actually got a kind side to him and is perfectly willing to accept demons that choose to be good, and even console them as Trish and Lucia can attest, and more or less plays Big Brother Mentor to Nero by the finale of 4.
Mao in Disgaea 3. Sapphire out right points this out near the end of the game.
The player can turn Morrigan into this. When Morrigan first joins the party, she's vicious, caustic, doesn't get along with Alister, and is absolutely against the idea of We Help the Helpless, making it difficult to perform altruistic tasks with her in the party without sinking her approval. However as the game progresses and if the player gets her approval high enough she begins expressing affection for him or her, and is more likely to go along with doing the right thing without (much) complaint. If the player succeeds in hardening her (or is it softening in her case) she will admit to genuinely considering you a friend, or if the player is a male character and romancing her, will openly admit to loving him (though also expressing confusion over what it means). The Witch Hunt DLC allows the player to take this to its full conclusion, with the right choices ending with the Warden and Morrigan staying together.
In Eternal Sonata, the Standardized Leader avatar character Allegretto is noted for being something of a Jerkass, but the PlayStation 3Updated Re-release goes a long way towards making him this instead by omitting at least one scene in which he displays some heavily jerkass behavior and heavily altering others or adding additional material to portray him in a more favorable light.
Ether Vapor 's main protagonist, Luca is surprisingly this. During the beginning of the game, he's the usual Jerk Ass, refusing to identify himself and his motives to his soon-would-be ally Sana and mocking Chaldean officers. That is until Teatree comes in where he tells her to bail out after her defeat and hopes she made it out. Justfied by the fact they both pilot mind-linked craft.
A few of the hunters from Evolve could be this, but the best fit is Slim. Initial conversations paint him as cynical and hostile to the others, but this is mainly due to his suspicion about being sold out for the bounty on his head and lingering fear of attachment due to PTSD. He eventually opens up, forming friendships with several other hunters and really becoming one of the group.
Cass from Fallout: New Vegas. She's got a foul mouth, drinks like a fish, and sleeps with anything with a pulse. But she's got a strict moral code and is extremely loyal to and protective of a Courier with good karma.
The Courier and the other protagonists from the franchise's other titles can certainly be played as this, by often using jerky dialog options but gaining good karma where it counts.
Fallout 4 gives us Paladin Danse, who's an interesting example. Like many members of the Brotherhood of Steel, he's something of a zealot, and views civilians with mild disdain and non-humans (that is, robots, Super Mutants, and ghouls) with racist loathing. Beyond his personal prejudices, however, he's one of the most morally upright companions available to the Sole Survivor: he approves of altruism and generosity, and will harshly rebuke the player for theft, extortion, wanton violence, and/or cannibalism.
Fate/stay night's most troperriffic character and more meme than man, Archer. He clearly means well and in a lot of ways is more successful at this than Shirou himself. However, in UBW the "heart of gold" gets restored to the surface... and promptly hit with a reset button. And then restored again.
FE 6 has both Hugh and his grandmother Niime (and their supports make it dead obvious). Chad and Rutger also count, as does Cath.
Hector from FE 7 is loud, brash, and reckless, but he's willing to abandon his lordly title and run away from home just to help his friends. Other examples include Legault, Vaida, Matthew, and Rath (though he's more "standoffish" than jerk).
Colm from FE 8 plays this trope so straight it's almost scary. Joshua, Innes, and Cormag also count, helped by the fact that they all have their own Morality Pet.
Innes acts like a complete asshole to the mercenaries he's hired in order to get them to abandon him and surrender so they'll at least survive. The mercenaries figure that out and say that they're staying around even after he fires them. After they save his ass, Innes re-hires them for double the pay they were originally getting. Douche, maybe. Well-meaning, certainly.
Then there's both Shinon and Soren from FE 9, though both can be seen as pretty tragic examples. Lethe and Sothe are also examples, and Naesala in a Magnificent Bastard sort of way.
Final Fantasy IV: Edge may be a perverted and arrogant ninja prince, who often flirts with Rydia, but his heart is in the right place at times.
Squall in Final Fantasy VIII is socially awkward, standoffish, and often quite rude, but underneath his emotional immaturity he's a decent kid.
Final Fantasy X: Jecht is egotistical, arrogant, a drunk, and verbally abuses his son on a regular basis. Then he goes to Spira, where he makes Braska and Auron help other people because "it's the right thing to do", even if it means problems for him and his companions. He quits drinking after an incident because he thinks his family wouldn't be proud. He records a video stating how much he loves his son and how proud he is to be his father, though eventually stops because he's "not good at those things". After reaching Zanarkand, we learn that he planned to raise his son to be a blitzball star, had it not been because he got to Spira. Then he sacrifices himself in order to give peace to Spira (if only for a while), giving up his hopes to get back home.
In Dissidia, he swallows his pride (for a while at least) and takes orders from Emperor Mateus because he promised him that he would get back to his home world with his son. Besides that we learn that if he insulted his son it was because he wanted Tidus to stand up and prove him wrong. We get a hint of all this at the beginning of the game: Jecht was well-loved by his fans, to the point a blitzball tournament is named after him when he disappears.
Auron also qualifies; throughout the game, he is the source of all things cryptic, he gives Tidus snippets of essential information (e.g. "Sin is Jecht.") while denying him any kind of explanation. He is aloof towards the rest of the party, and is particularly determined Yuna finish her pilgrimage, despite what it'll mean for her. Then it turns out he looked after Tidus for several years before the start of the game as a reasonable Mentor, and he was pushing Yuna and especially Tidus so hard because he wanted them to break the eternal cycle and truly destroy Sin. And it works.
Lulu initially treats Tidus extremely poorly, rarely even speaking to him, aside from snark and a little bit of exposition. Later, it becomes apparent that she's just hesitant to open up to people because of a painful past (the death of her first summoner, and losing her First Love come to mind). Eventually, she opens up to the player, eventually developing Mama Bear tendencies towards Yuna, Tidus and Rikku. Coincidentally, it's around the time Yuna and Tidus' growing attraction for each other becomes blatantly obvious.
Final Fantasy XIII: Lightning is a moody, distant young woman who spends the opening hours beating up and abandoning her party. Then you get the background as to why she's like that, and she noticeably softens up from then on.
Ryudo, from Grandia II, fits this trope to a tee. He starts off as a devil-may-care, potty mouthed jerk who only seems to be going along with the quest for money, but later reveals that most of it was just a bit of a coping mechanism, due to the rather low opinion most people have of mercenaries in his world. By the end of the game, he's transformed into a pretty likable and friendly guy, albeit one who can still curse like a sailor.
Sweet in Grand Theft Auto: San Andreas constantly criticizes his brother, CJ, and blames him for the death of his brother and mother when he ran away to Liberty City. Sweet does eventually ease up and gives his brother his support in a big brother love kind of way.
Gadd from The Guild Wars expansion Eye of the North. He starts out as a complete jerkass, bossing the player's group around, mocking you in a very condescending manner, and often repeating things IN CAPS in case you "weren't listening". At the end of the G.O.L.E.M. mission, Oola arrives, saying she has bad news. A confused Vekk asks what Gadd is upset about now, to which Oola sadly replies, "He was trying to boost the power of the last Golem. There was an explosion. He didn't make it. I'm sorry". In other words, he (perhaps knowingly) sacrificed himself to give your team a better chance of surviving. Suddenly, he doesn't seem like such a bad guy afterall...
A fairly common character archetype in the Harvest Moon universe, enough so that listing every example could take a while. In random villagers, it tends to be more prominent in Grumpy Old Man-style villagers who develop a curmudgeonly respect for you (such as Galen in A Wonderful Life and DS), while in bachelors and bachelorettes, it tends to go hand-in-hand with the Tsundere archetype (such as Gill in Tree of Tranquility/Animal Parade, and some incarnations of Karen).
The House of the Dead: OVERKILL has detective Issac Washington who swears like a sailor (to the point of almost single-handily breaking the Guinness Book of World Records), is quite crude, and is introduced by cold-cocking G in the intro cutscene. In the end, G suspects that he puts on a though-guy persona, but cares deeply for G deep down. Washington doesn't object to this.
Similarly, Samos the Sage can be a total jackass at times, but in the end he genuinely cares about the other three main characters (yes, even Daxter).
Daxter snarks at everyone and repeatedly tries to weasel out of trouble, but he genuinely cares for his friends and risks his life repeatedly for them. Torn is a very bitter man who repeatedly berates J&D and periodically sends them on unpleasant and/or borderline suicidal missions, but he dropped his Krimzon Guard commission like a rock in order to do the right thing. Sig is a ruthless mercenary who's always willing to put his life on the line for his friends. Naughty Dog loves this trope.
Subverted, almost, in Jewel Knights Crusaders. The main star makes it abundantly clear that he is Jerk almost all the way through. Whenever he shows the tiniest bit of kindness, he subverts it. Except a couple of times when he doesn't.
Yuuichi in Kanon. Despite practically being a less cynical Kyon who doesn't keep his comments to himself, in reality he's very dependable.
Dark Pit is supposed to be the manifestation of all of Pit's negative traits, but Pit himself is so inherently kind that the only "negative traits" Dark Pit represents are Pit's stubborn streak, brashness, arrogance, and a sarcastic sense of humor. Despite all that, Dark Pit himself is not completely evil and can be just as heroic as Pit when properly motivated.
Viridi starts off as a plain Jerkass when she first appears. She's bratty, short-tempered, and argumentative. But as Character Development kicks in and she's forced to aid Pit later in the game, she begins to warm up to him.
More than one in The King of Fighters... starting with The Protagonist himself, Kyo Kusanagi. he's brash, arrogant, loud-mouthed, snarky and fully of himself... but he also genuinely cares for his family and friends (specially his girlfriend and his Cool Big Sis of sorts), and Heaven help you if you hurt them. Not to mention the semi-canon KOF: KYO media lets us see how he behaves in his daily life, and even reveals some hidden insecurities that he must deal with.
The influence system means you can nurture the heart, or crush it under your booted heel, depending upon how badly you give in to the Videogame Cruelty Potential.
Jolee Bindo from the first game.
The first game also has Bastila (though she is only really a jerk to the player and Carth) and Carth (just watch all the arguments over trust).
Joel from "The Last of Us". He starts out as a huge jerk in the beginning of the game, mostly due to his Cynicism Catalyst, (a.k.a Sarah's death.) But, as the game progresses, his heart of gold shines through with his new found relationship with his surrogate daughter Ellie.
Herschel Biggs from L.A. Noire is not the most sociable character to be partnered because he works alone. However, near the end of the second Arson case, he begins to like Cole.
Francis from Left 4 Dead. He hates almost everything except vests, and his background info shows that he is a rebel and enjoys the zombie outbreak because he can now kick some ass without the law standing in this way. During the game, he loves to bust Bill's chops, but shows respect if Bill happens to die. He also shows a bit more emotion to Louis if he gets killed, saying things like "He didn't deserve this." When it comes to survivors being low on health, he shows the most concern to Zoey, and if any survivor is incapacitated twice, Francis will express grave concern for the victim as he helps them up.
Rochelle of Left 4 Dead 2 will say this almost word for word about Nick in the sequel if he pulls her up after she's fallen from a ledge.
Francis shows more "gold" than "jerk" when it comes to talking about Bill's death in The Passing, referring to Bill as a good man and how he would have shot Nick for being so disrespectful and rude.
Nick himself has shades of this. While he starts off as an extreme Jerkass, he does seem to become more friendly with his fellow survivors during the course of the game. For example, sometimes when Ellis dies, he'll say "You know all those things I said about you, Ellis? I was joking..."
Gala from Legend of Legaia starts out as a Jerk with a Heart of Gold. He constantly insults Vahn and Noa at first, demeaning their violent ways and quite openly displaying his disdain at being forced to help them. Eventually, he'll lighten up and become friendlier with the rest of your team, though he still occasionally argues with Noa.
Mido from The Legend of Zelda: Ocarina of Time starts off as the only Kokiri who hates Link, to the point that he spreads rumors that Link was the one who was responsible for the Deku Tree's death. By the time you meet him again as an adult, he has begun regretting his mistreatment of Link, and he asks Adult Link (who he does not recognize as Link) to convey his regret to Link if possible.
The Man From The Curiosity Shop sees nothing wrong with blatantly selling stolen goods, and is rather racist to anyone who isn't human, but he seriously cares for Kafei. It's especially telling that Kafei went to this guy for help rather than his own parents when he was cursed.
In The Legend of Zelda: Twilight Princess, Midna, at the start of the game at least, is an abusive, snarky, whiny brat who wants only power and revenge, but she eventually begins to let slip a few signs of her soft spot for Link (by the end of the game, she's not even trying to hide it).
Linebeck from The Legend of Zelda: Phantom Hourglass also counts. At first, he's a selfish coward who is taking advantage of Link to find treasure. By the end, he saves Link's life and gives up unlimited wealth to have his old boat back.
Groose from The Legend of Zelda: Skyward Sword starts off trying to sabotage Link's chances in the Bird Races by locking up his Loftwing and then having him and his lackeys ram into and throw eggs at Link in the race itself, all so he could get to be the one to go out with Zelda. He's eventually shown to be quite noble when the situation calls for it, though; most notably, he helps Link fight the Imprisoned with a bomb-launching apparatus that he built specifically for that purpose, and he warms up to Link over the course of the game.
If Nash was a borderline case in the remake, he WAS this trope in the original. He might have been egotistical and frequently abrasive, but he goes quite far out of his way to help Alex out and is one of the few people in Vane to recognize that Mia is actually quite stubborn and strong-willed underneath her sweet personality. By pretending to switch sides, he gets the team to the Frontier, and nearly dies for it when Xenobia figures out what he's up to. He goes from annoying to downright heroic.
Ghaleon also may count in this category. He was the main villain in the first game and one of the last bosses in the second game, but his long-winded death speech, gift of an ass-kicking sword, and a couple of fairy gardens show you he really did mean well.
In Marathon, a rampant Durandal was the Big Bad. In Marathon 2, he's mission control. In Marathon Infinity, he saves the player rather than himself from imminent death - twice. And he died permanently both times. And Durandal's driving ambition in the first two games? To make himself immortal, no matter the cost to anybody else.
Similarly, Wrex in Mass Effect is the most cynical and jaded of the party members. However if the player helps him reacquire his grandfather's old armor he'll note during his Heroic B.S.O.D. that Shepard's done more for him than any of his family. If he survives for the sequel, he becomes the Overlord of the Krogans of Tuchanka, determined to drag them kicking and screaming into a new future. He also happily greets Shepard upon meeting him/her, noting that their time spent was one of the best times of his life. He is almost 1000 years old.
Commander Shepard is capable of fitting the trope as well, depending on the player's choices. It's a good way to rack up paragon and renegade points at the same time.
Javik from the From Ashes DLC morphs into one over the course of the third game. (A very drunk) Tali even calls him out on it, commenting that despite his aloofness, rudeness and Cultural Posturing, Javik has obviously become fond of the rest of the squad, especially Liara, and has come to have particular respect for Shepard, despite their almost completely opposite methods if Shepard is a paragon.
In the Omega DLC for 3, Paragon Shepard and Nyreen can nudge Aria T'loak into this territory.
The Bonne Family from Mega Man Legends. They're willing to lay waste to cities in the pursuit of treasure, but when an island of people is going to die they drop everything to help out. In the sequel they steal everything that isn't nailed down from Saul Kada except the toilet paper, because they can't bring themselves to go that far.
Tiesel: Take everything that isn't nailed down! I don't even want a toothpick to be left!
Serv Bot: We've loaded all the food, money, and supplies on board. What should we do about the toilet paper?
Omega-Xis from Mega Man Star Force. He starts out viewing humans as blundering inconveniences, but does come to genuinely care for his host as a friend. He also shows genuine horror in 3 when Luna is temporarily deleted by Joker, and when Ace and Acid sacrifice themselves to save him and Geo from a self-destructing Joker.
Axel isn't the nicest person but he does genuinely care for his friends. When the others start joking around during the shelter segment, he scolds them for not being worried about Petra's safety.
For all his insults and jibes, Magnus is still a decent guy underneath it all.
MOTHER: Gang leader and misguided youth, Teddy. After initiating a tussle with Ninten, Teddy joins up with the party and helps greatly with their quest.
From EarthBound, we have Mr. Everdred, a thief who jumps from a roof to attack you. However, after beating him (or not), he tells you to come back after rescuing Paula, at which point he gives you ten thousand dollars. You're supposed to use the money to help the Runaway Five, though, so you don't get to spend it. Awwww.
Fassad/Yokuba from MOTHER 3. For pretty much the entire game he's been a Jerk Ass in various ways- torturing Salsa, corrupting Nowhere Islands, and if it weren't for him, the REAL Jerk Ass, Porky/Pokey might have died from the start, (depending on if he's really capable of dying) and would not have succeeded in manipulating the islands' inhabitants anyway, and also, he wouldn't have gotten the idea to pull the Needles in the first place. But you figure out that last one right as you discover that Fassad/Yokuba = Locria. (That explains why he's so ugly) And his room is in the classic Magypsy style. Then Pokey/Porky goes on the intercom and says get out of there. And right in the next room, there's a little mouse. He says, "Squeak squeak squeeeak. (I don't think Locria is coming back anymore. Oh, me? I'm a mouse Locria liked to dote over. He had a creepy "Nwehehehehe" laugh, so he might've seemed like a mean person in most people's eyes, but he was very nice to me, at least. Do you think he'll be coming home soon? I'm so lonely.)" Considering you humiliated him, made him reconstruct himself, left him to drown in sewage for hours, and since your ultimate goal is to pull the Seventh Needle, effectively killing him once and for all, it may make some feel guilty for leaving this little, insignificant mouse all alone. Even for killing the Jerk Ass.
Neeshka can be a bit of a jerk, but a careful player can bring out her softer side. Likewise, Gann in Mask of the Betrayer comes across as an arrogant, uncaring person, but is revealed to be quite the opposite if a female character gets enough Influence with him.
Oswald of Odin Sphere is another example. Only shows his nice side to people he trusts though.
Another example may be Hidetoshi Odagiri as, though he is strict, stern, and often cold to most, eventually shows signs of holding a heart of gold as he truly believes that upholding the law will help everyone in the end. At the end of his S. Link, he decides that he wants to try being softer and ask others for their opinions. He even makes it clear that he's thinking about becoming a teacher in order to help set the foundations for a better future and admits that much of his previous jerkish behavior was naive. Sure, he's a hardass, but he's also got very good intentions at heart. In fact, it's implied that he only ever wanted so much power so that he would be able to help, and promote fairness for, as many people as possible. Huh.
Kanji Tatsumi from Persona 4 is a rather awkward nice guy with a bit of a temper, who acts like a delinquent. At one point he threatens to tear down Chinese Diner Aiya because the manager misplaced his order… before Kanji corrects himself and adds that he'll rebuild it twice as good; he's gonna RENOVATE his ass.
Kanji also likes to sew and makes stuffed animals (very well made ones at that).
Yosuke Hanamura counts as well. He likes to poke fun at the rest of the team, Kanji in particular, but he's a good guy who truly wants to help his friends and save his town (at least eventually: his Shadow points out that he wanted to look into things initially because he was hoping to be a hero).
Kinshiro Morooka, a.k.a "King Moron", might be a subtle example. He's a rather snobbish (and hideous) man with a grudge against women as well as the main character. He treats his students rudely (putting the main character on his "Shit List" within minutes of meeting him), and got flat ass drunk on the school field trip. However, Conversations with some students in the school reveal that he's dragged several girls into his office for "private talks"… in which he advises them on their career paths and urges them to follow their dreams. It's likely that he genuinely cares for his student's futures, but really doesn't know how to properly show it. Of course, you wont find this out unless you actually take the time to talk to NPC's walking around school.
N from Pokémon Black and White. At first, he seems to be a driven jerk who hates humans and only cares for Pokemon, even calling out Professor Juniper on having nothing against relationships between the two, and that he is revolted by even the idea of the Pokedex itself. But at the end of the game, it is revealed that he didn't think there were Pokemon that liked humans, even though he himself could talk to them - he'd been raised with Pokemon abused by humans. And it turns out his constant battles with you were (unsuccessful) attempts at confirming his beliefs.
The Prince of Prince of Persia: The Sands of Time (before the sequel, anyway) is arrogant, spoiled, sarcastic, reckless, stubborn, and obsessed with 'honour and glory' to the point where he accidentally unleashed hell for it, but he is also very brave, well-meaning, and totally, heartbreakingly desperate for his father's approval, even though his father obviously already adores him.
His later counterpart in Prince of Persia (2008) is a scruffy, cynical, selfish, irreverent, hedonistic, blatantly lecherous, grave-robbing lout. He's also pretty friendly when he wants to be, especially to girls he likes, and quite soft-hearted. In the end, he proves that he'll do anything to save the people he loves, including saving the world... and personally bringing about its end.
Jake in Resident Evil 6. He's the master of snark, and can't seem to go 5 minutes without a sarcastic comment. Plus, let's not forget he's a mercenary. And yet, he risks his own life to save Sherry countless times, and in the end, takes back his demand for 50 million dollars in exchange for his blood (which will save the world), and instead says 50 bucks will do. Also, in a hidden cut scene after Ada's campaign, he helps a middle eastern boy by saving him from several huge B.O.W.s in exchange for a mere apple.
Capelli in the end of Resistance 2. He eventually goes to this in the third game.
Knuckles the Echidna is one of the most prolific examples. He is shown to be quite rude, hot-tempered, and anti-social, but he's also been said to have "a trusting heart, and wants to believe there's goodness in everyone" and can prove to be a helpful hand for Sonic and the gang. This element of his character really comes into play in Sonic Adventure 2, when he saves Rouge from falling into the lava and then actually apologized for hurting her. In Sonic the Hedgehog (2006) he was noticebly upset when Sonic was temporarily dead. His trait also spilled over into most adaptations, such as Sonic the Comic where he cheerfully helped Tails' Fake Ultimate Hero scenario by pretending that he was Sonic, and that he was Tails' sidekick. Knuckles is also generally a nice person when he's in a good mood.
Sonic SATAM has Antoine, who although being a cowardly, pompous oaf has proven to be unquestionably loyal to Princess Sally, and on occasion shown traits of Crouching Moron, Hidden Badass when one of the others was in trouble, like when Sonic was about to be ambushed from behind by a Nasty Hyena. The comics gave a few more redeeming moments such as a very early example of when the Freedom Fighters thought Sonic was dead, Antoine cried out that Sonic would be avenged.
Later in the Archie Comics, Ash the Mongoose was introduced. From his first appearance, he had a grudge against Sonic, (though some say his reason for hating Sonic wasn't good enough )and was outwardly bitter. The 'heart of gold' part of his character came out when he risked his life to save Mina from a bomb in her dressing room.
Some of the game manuals claim that Sonic is one of these (being short-tempered, but very heroic at heart), but it's almost never canon in-game at all. Then again, the "heart of gold" is more emphasized than the "jerk" part as he is always nice to his friends while is cocky and snarky towards his enemies. The Archie Comics tend to focus on his "jerk" side more often than his in game appearances but avoids making him a complete Jerkass like his Sonic the Comic incarnation.
Shadow the Hedgehog is more than willing to fight the other heroes should they get in his way and pretty apathetic to things that don't relate to his goals, and can be quite of a rude and egotistical Jerkass at times, but he's always at the frontlines whenever a new threat arises and is capable of working with the heroes too when they're on the same page. He also cares very much for his two teammates, and his late surrogate sister Maria, not to mention that he cares for the well being of everyone else (even Sonic), even if he doesn't always express it.
Rouge the Bat is a selfish, vain seductress who feels all of her gems are hers to keep, but she's capable of expressing gratitude when someone helps her and shows genuine concern for her two comrades.
In Star Ocean: Till The End Of Time, you have as an optional character Roger S. Huxley, a Menodix (essentially a small boy with a racoon's tail). For most of the game, he alternates between being a jerk and immature (although he is only 12). But should he (re)appear in a later cutscene where he is injured after destroying a transporter jammer (which character does this out of Nel, Albel, or Roger is decided by the player's choices earlier in the game), it turns out that for all his flaws, his heart is in the right place. This same scene could be considered a moment of heartwarming.
Karin Kanzuki, although this side is more apparent when she's not fighting. She makes friends with her longtime rival Sakura, and in Rainbow Mika's storyline, Karin agrees to provide some of her vast fortune to support Mika's wrestling career.
Dan Hibiki might be an obnoxious Miles Gloriosus who gleefully takes credit for other people's work and fancies himself a much better fighter than he [[Joke Character actually is while secretly despising people "cooler" than him, his heart is in the right place and his intentions are good, allowing him to become friends with both Sakura and Blanka.
And from the same game, Tear Grants can be very icy and blunt at times, but she noticeably softens up as the story progresses.
Even Luke, the main character, starts out as this before his Important Haircut and Character Development. And Asch keeps it up for the whole game, although the emphasis there is on the "jerk" part.
Natalia is a true Royal Brat who routinely bosses Luke and Guy around and only gets to join the party by blackmailing Luke. She is also responsible for many humanitarian and philanthropic works throughout her kingdom and doesn't hesitate to use her Healing Hands if she sees someone suffering in front of her. By the end of the game, she's lost the jerk part entirely.
At first, the mercenary Kratos in Tales of Symphonia appears to be traveling with the party only for the money, and then on top of that he betrays you! But, it turns out he's not as much of a jerk as Lloyd first thinks and he comes back to your side in the end.
Zelos fits this trope even better. While he is a teasing, arrogant and carefree Handsome Lech who starts off with a dislike for half-elves, he does make a clear effort to overcome that prejudice and even uses his status to prevent new laws that would further the horrible treatment of half-elves from being passed. He also shows genuine concern for Sheena, and he cares deeply for his little sister despite the fact that her mother murdered his. Actually, much of his actions during the game are for the sake of his sister because he believes the fact they sentenced her for something she didn't do to be unfair. Also, like Kratos, he betrays you at one point but comes back to yourside in seven of the eight endings. Even in the one where he doesn't rejoin he he helps you one last time before he dies. When conditions place him closest to Lloyd, he also shows that he believes that Lloyd was right that status and race mean nothing.
Yuan from the same game is a borderline example. He's cold, standoffish, and generally impatient with the main cast for the entire game, refusing to acknowledge them as anything but grudging allies...when he's not actively trying to kill them. But it turns out that all his actions are pushing toward a goal of trying to save the world from the Big Bad, and grant Martel, his fiancee, the peace she deserves. There's a sidequest near the end in which you return the engagement ring he dropped in a mandatory cutscene early in the game, at the end of which he's willing to literally beg Lloyd to give it back to him.
Yeager of Tales of Vesperia is a minor recurring villain with a German accent, crazy speech, and constantly meddles in things on both sides of a conflict so he can keep the profits coming in as a weapons dealer. Then Raven sees fit to inform that he's just laying the nutjob act on a little thick. THEN you find out he's been donating to an orphanage all this time and raising two of the orphans like his own daughters.
Miguel Caballero Rojo in Tekken 6. He is a jerk to everyone except his sister. When he found out about her plans in marriage, he tries to murder him, but relents anyway for the sake of her happiness.
Anna Williams, to a somewhat lesser extent. Sure, she's an assassin with a blood feud against her sister Nina, but she's nowhere near as brutal about it as Nina is and there are strong hints throughout the series that, deep down, she wishes their rivalry could just end.
Dr. Neil Watts from To the Moon. At first, he's a total smartass and enjoys being sarcastic, mean and doing INCREDIBLY stupid things (like riding a horse backwards), but when it comes to Eva trying to move River from Johnny's memories so he can go to the moon he FIERCELY tries to prevent that, believing that that would make Johnny miserable, proving that he does in fact care!
Hakurei Reimu of the Touhou series is occasionally played as a Stoic Jerk with a Heart of Gold, when the fans aren't joking about how her approach to solving a problem is thuggish (or genocidal).
Many Touhou characters can be considered like this. Of course, sometimes it's really "obnoxious with a heart of gold", or "lazy with a heart of gold", or "utterly crazy but with a heart of gold".
Teagan from Uncommon Time is a very dark and borderline deconstructionist take on this. She is motivated by a genuine desire to protect Alto and look out for her best interests, but the stress of fighting against Alto's powerful family and dealing with Alto's Stepford Smiler tendencies made her snap, and she now dismisses Alto as a Broken Bird and an idiot who can't think for herself. Her belligerence doesn't stop at Alto, either, and she's particularly mean to Meirin. To her credit, when Alto finally snaps and voices all the resentment she's kept bottled up, Teagan immediately has a My God, What Have I Done? moment and profusely apologizes. She becomes much less hostile after this and makes genuine attempts to be friendlier with the rest of the cast. Alto still refuses to forgive her for the years of verbal abuse, however, saying the damage has already been done.
Tenmyouji in Virtue's Last Reward. He's a Grumpy Old Man to the core who isn't afraid to call it like he sees it; he also won't hesitate to choose "Betray" in the AB Game. But... everything he does, he does for the benefit of his grandson, Quark. And although it takes a while for him to warm up to others, he's an extremely steadfast and true friend once someone earns his trust. His curmudgeonly attitude might have something to do with the fact that he's been chasing his lost love all his life...
From Wild ARMs 3: Maya may seem harsh, but beside the obvious motivation of wanting to get rid of other Drifter competitors, she does have a sweet spot for Virginia, protecting her in her own way (and literally saved the party's life at least once).
Neku Sakuraba of The World Ends with You hates people in general and at the beginning of the game does his best to shut them out. But after playing the Reaper's Game for 6 days he starts becoming a lot more friendly and tolerant.
Haseo from .hack//G.U. starts as grade-A Jerk Ass in .hack//Roots, slowly develops into this throughout the game, and by the end of Volume 3, he apparently has dropped his jackassery.
In Yu-Gi-Oh! Reshef of Destruction, Weevil is portrayed as this. He gives up Insect Queen to help the player and decides to show up to greet the player (but he keeps insisting that it's to get his card back).
Agate Crosner of the The Legend of Heroes: Trails in the Sky trilogy. He first comes off as this when he confronts Joshua's team, but gradually develops into a respectable fighter. More so that he develops into a big brother figure to the team. This is due to his time being with the Ravens. He was their leader.
Charles the candy store owner in Delicious 4: Emily's Taste of Fame yells at everybody who walks into his shop and makes cracks at the title character's weight and perceived uselessness, but also offers to clean tables in order to lighten her workload and chews out her best friend Francois for not lending her a hand himself.
Johnny Cage from Mortal Kombat, especially in the new timeline established by 9. He initially comes off as an insufferable movie star with an overinflated ego, and spends his entire chapter in 9 making a complete ass of himself, hitting on Sonya much to her chagrin. But he is horrified at the idea of killing a defeated opponent, and later on good naturedly brushes off Jax beating him up towards an argument. By the time of the sequel, he's considerably mellowed out, and is an affable and approachable mentor to the new generation of heroes, and keeps Sonya fromgoing too far. He's also an endearingly doting and understanding father to Cassie Cage, and possibly the series' best dad.
Tubbs from Neko Atsume often comes in to gobble an entire food bowl, leaving none to share with the other cats. However, they do leave a large amount of silver fish if they're left alone to digest their meal rather than forced out, their memento is a food item (fish jerky) that they actually held back from eating, and once in a while if you have the giant cushion out, they'll take only the usual small amount of food and then rest on the cushion.