Junichi Sato seems to really, REALLY like this trope in the anime he directs:
Mamoru Chiba, the title character's love interest in Sailor Moon, starts out as a Deadpan Snarker who enjoys teasing Usagi about everything.
Subverted for Makoto Kino/Sailor Jupiter from Sailor Moon. Similar to the Toradora example earlier, several people assume she's a violent bully, but she's actually very sweet.
Initially played straight with Haruka Tenoh/Sailor Uranus. She may be harsh towards the Inner Senshi, especially Sailor Moon, but after Sailor Moon saves Hotaru from Pharaoh 90 while sacrificing the Holy Grail in the process, and later proves herself against Uranus and Neptune, Haruka finally accepts Usagi's fate as Messianic Archetype.
Fakir, the jerkish, controlling guardian of Mytho in Princess Tutu, who turns out to be using the tough exterior to hide his fear of being killed in service as Mytho's "Knight" and being a failure in the end.
Layla Hamilton from Kaleido Star, the Broken Bird who is as tough on herself as she is on new recruits to the Kaleido stage and has quite the daddy issues.
Many characters in Axis Powers Hetalia act like this at some point or another, being jerks to each other during conflicts but genuinely showing kindness and concern for younger nations, animals or their subordinates: America, England, France, Germany, Austria, Prussia...
Byakuya Kuchiki from Bleach. He is shown to be very arrogant and snobby (possibly to do with his noble family upbringing). However, he has been proven on more than one occasion to be fiercely devoted to his sister, Rukia.
Same goes for his lieutenant, Renji Abarai, who is just as devoted to Rukia as well as very Hot-Blooded and loyal to those he cares for.
Kensei Muguruma. He and his lieutenant Mashiro get along like an ice cube and the sun, but when Wonderweiss started beating the shit out of her, the first thing Kensei did was go and save her. And then deny that was his intention. He also saved Hisagi from a Hollow when he was young and tried to get him to smile, although he did it in a hilariously frightening manner.
Moe Shishigawara and Riruka Dokugamine.
Guts from Berserk qualifies. He's violent, cruel, cold, and obsessed with his personal goals, which are often achieved at great cost or risk to others. But unlike his nemesis, he genuinely cares about the people around him, is a compassionate leader, and his distant, uncaring demeanor seems to come from a desire to keep people away from the danger he's constantly in. It ... doesn't always work out that way. But he tries.
Dola from Castle in the Sky. She's a crusty, tough-talking old lady who is abrasive, bossy, and even controlling of her boys. She even tries to kidnap Sheeta (and steal her crystal) at the beginning of the movie. Later on, she grudgingly agrees to let Pazu help her save Sheeta and agree to take them aboard her ship. (While she's playing chess with her husband, who questions her about her affections for the kids, her response is, "Whaddaya mean by that, ya old fool?! I'm after treasure. That's all." Deep down, however, she's actually a softhearted person who comes to admire Pazu and Sheeta for their loyalty toward each other. (She does a brief double-take, though, when she overhears Pazu telling Sheeta that Dola is "much nicer than she pretends to be.")
The Shinka in the anime for Chuunibyou Demo Koi ga Shitai! is this. Specifically, no matter how abrasive she is towards everyone at the club, the fact that she joined their beach vacation is a telltale sign that she's far friendlier to them than she'd ever like to admit. This is especially highlighted in Episode 9, when she actually gives Rikka advice on romance.
Tomoya Okazaki from CLANNAD. Yes, he tries to project the front of a lazy ass who delights in twisting the truth for practical jokes on anyone and everyone (leading to some impressive amounts of confusion and misunderstanding among the more naive cast — Nagisa especially), and tries to look all though and detached. Yet he ends up trying to help the mains of every arc, without a second thought, and has been seen to drop Manly Tears, or openly crying in frustration and sadness, at the endings of some.
Lelouch. Normally he's a snarky Magnificent Bastard who calls concepts such as "justice" and "honor" jokes and talks down to most people. Despite this, he goes out of his way to protect and look after those close to him, even his best friend-turned-rival and his Mysterious Waif partner with a Sugar and Ice Personality.
Mad Scientist Lloyd cares about his Knightmare Frame more than people; openly mocks the royals (and, well, everyone else too) and generally seems to have absolutely no respect for rank or privilege (though he possesses both); proposes to Milly just so he can acquire her Knightmare Frame (and then never mentions it again); and even teases Suzaku when he's extremely unhinged about Euphemia's death (to be fair, he may not have known much about Suzaku's feelings, but still). However, he also took Suzaku on as a pilot for the Lancelot, at a time when discrimination against Japanese people was commonplace; and he and Cecile come to the rescue of the Ashford students when they're held hostage by the Black Knights.
Lorenzo. While he constantly torments Ian, treats Marjorie like a child, and cheats on Claire with Pascal, he has some redeeming moments. He comforts Nadia when Ian falls for Jeremy, even attempting to confront Ian about it, tries to convince Claire that Marjorie should be given more freedom, and also rescues Jeremy from Pascal's drug induced abuse.
In a lot of ways Ian also fits this trope. He does care about Jeremy, but often the ways he goes about trying to help are off, and he gets too angry at Jeremy's failures too easily.
Kurosaki/Daisy from Dengeki Daisy definitely qualifies. In person, he's rude and obnoxious. Over the phone... not so much.
On a much smaller scale, Yajirobe. A belligerent glutton who vocally wants nothing to do with the other Z-Warriors, he still always ends up coming to their aid when they really need it.
Rouce, a.k.a. Red Lightning a.k.a. Mink's father in Dragon Half. A once-renowned warrior whose recent "exploits" consist of fighting his dragon wife, hitting on any attractive woman (regardless of her availability), faking life-threatening diseases to get out of hunting for food, and pulling down his own daughter's pants, it seems the only thing he's good at now is lying. However, he does get a moment of off-panel awesomeness singlehandedly slaughtering a horde of monsters about to eat his wife and daughter. Though he appears to be sleeping when the two return to camp, the blood on his sword (and trademark "R" cut on the monsters' corpses) make it pretty clear that he's the one who saved them.
Shizuo Heiwajima from Durarara!! acts like a complete Jerk Ass at some points, but it turns out that, when you don't activate his Hair-Trigger Temper, he's actually just a socially inept sweetheart. He deeply cares about his brother and basically anybody who isn't Izaya Orihara.
Youichi Hiruma, from Eyeshield 21. He never refers to anyone by their real name, only by his personal nickname, and all his personal nicknames start with "fucking" (toned down to "damn" in Viz's translation of the manga). (Sena is "Fucking Shrimp", Mamori is "Fucking Manager", and then there's his best friend Kurita, "Fucking Fatass", and so on.) He's a violent gun nut who slings a constant string of verbal and physical abuse on his team, uses blackmail to get his way like some people say "please", and lies like it was going out of style. He also never fails to reward perseverance, dedication, and effort as long as the team doesn't suffer for it, has his own unique brand of showing affection which he doles out with regularity, and puts himself through all the same crap thatworse crap than he puts everyone else through.
One notable scene was when an exhausted Yukimitsu made it to the top of the Tokyo Tower, as part of Hiruma's tournament to get more teammates. However, Yukimitsu's bag of ice, that he was suppose to bring up to the tower, had all melted. But secretly, Hiruma slipped in an ice cube and congratulated him for making it.
Another example is when an enraged Gaoh was rampaging in the stands looking for someone who insulted someone he considered a Worthy Opponent, Hiruma jumped in front of Mamori and Suzuna to protect them from harm.
Agon at the end, shaving his head to give Unsui inspiration to play for himself.
Linebacker Habishira. Mostly out of blackmail, but even after being released by Hiruma so they can practice, they still help Deimon out a lot.
Marco. All he wanted to do was win the Christmas Bowl for his girlfriend, Maria, and show her the rising sun after the victory, but lost sight when Maria disproved of using Gaou as a weapon.
In Freezing, the third years may be major, major jerks who were obsessed with beating the crap out of the main character for unjustified reasons, but they're still soldiers trained to save humanity from Eldritch Abominations. During the Academy Siege, they were in the front lines covering for everybody else.
Kyou Sohma from Fruits Basket. Despite being a jerk to everyone, he develops great affection for Tohru, whom he eventually falls in love with.
He hates Yuki, but he does seem concerned when the latter collapses because on an asthma attack. Also, he clearly cares for Kagura despite her Tsundere/Yandere tendencies towards him.
Edward Elric acts like a jerk to many characters - including his younger brother Alphonse, who constantly has to apologize for him in the trend of "Don't take it personally, he's like that with everybody and he's actually nice deep inside."
Greed might also belong to this category. He doesn't seem to be as selfish and insensitive as he claims to be and is occasionally quite serviceable.
Roy Mustang makes it into this category as well, frequently appearing callous and arrogant to those (Ed in particular) who don't understand his past and/or motives.
Olivier Mira Armstrong could also fit in this category.
Takuto, the male protagonist of Full Moon o Sagashite, is a mild example (bit moreso in the manga) of Jerk with a Heart of Gold, as his mannerisms are rather limited to his way of speaking to others. Occasionally rude, anti-social, and snarky ("baka" is his favorite word) he will always say the exact opposite of how he truly feels, yet when nobody's looking, he'll do something incredibly sweet. Just make sure you don't blink because you'll miss it. Because of an overwhelming number of "tsu-tsun" traits, he can also be classified as the Type A male Tsundere. By the end of the anime series, his jerkish side pretty much vanishes for his last action is to sacrifice his life and soul to save Mitsuki from her cancer. A heart of gold as well as it can be defined indeed!
Naoki Shinjyo started out as a Jerkass when he lashes out at his team's mechanics and has gets angry over his poor driving skills despite being The Ace, but once Miki Jounouchi blames him for having no respect towards mechanics and he proves himself as a true racer, he begins to show more of his softer side.
Karl Lichter von Randoll also started out as a arrogant racer when he puts down other racers, saying that he's better than anyone, but after the race with Hayato in the Spanish race that ended in his defeat, he slowly softens up and begins to have a sense of chivalry.
In Gakuen Babysitters, Chairman Morinomiya, despite coming off as a cold, old woman most of the time, has shown many instances to be very kind and caring toward her adoptive grandchildren. Even during times where she would vent her busy schedule, after receiving an invite from Kotarou for a play she immediately had things rescheduled so she could attend.
Midou Ban in Get Backers has a mocking nickname for nearly everyone (monkey trainer, thread spool, computer boy, etc.), is selfish, sneaky, gropes women constantly, and is generally just not a nice guy to be around... unless your name is Ginji, and you get to see that "Ban-chan" is really just a cuddly, misunderstood dork.
Chiharu Eniwa of manga series Girl Got Game is one. Almost as soon as he meets Kyo, he fights with "him" and constantly shouts at and argues with "him." He does have a short temper, but he's actaully nicer than he lets on. When he does help someone (usually Kyo), he'll often give the usual "I'm only helping so you don't get mad at me later," or some other half-hearted excuse.
Several characters from the Gundam franchise fit in her perfectly.
Shin Asuka from Gundam SEED Destiny certainly fits into this trope well. He initially seems to be a troubled youth with authority problems and chews out anyone who tries to help him in most ways, but also is more than willing to take care of Stella — long after she's discovered to be an enemy pilot. As the series goes on, it becomes more and more obvious about this, but that doesn't stop the fanbase from pulling a Flanderization on the guy and making him 'emo.'
Yzak Joule, after some well-deserved character development: aggressive, stand-offish and generally a Jerkass, he expresses care for Athrun when he's reassigned ("Don't get killed until then..."), and although he's still pretty aggressive by the time SEED Destiny rolls around, he's covertly working for Lacus.
Kamille Vidan Yes, the girly-looking and girly-named boy has hugeWangst and can be a big Mood-Swinger, but he also genuinely cares for those he loves and tries to help them.
His rival Jerid Messa is also one, though quite more brutal. Basically, he's a huge Jerk Ass, but if you do manage to make him care for you, he'll genuinely do so... and it will be your downfall
Amuro Ray, a paranoid anti-social kid in the heart, and a hero in every sense of words.
Van of GUN×SWORD: got a town that needs saving? He'll dismiss your plea because it has "nothing to do with" him, but then he'll think better of it, especially after his Morality Pet Wendy prompts him a little (or gives him an outright scolding). Speaking of Wendy, he takes her for granted much of the time and occasionally treats her rudely, but if she's sick, in danger, or even just unhappy, he can be surprisingly tender towards her.
Mamoru Takamura in Hajime No Ippo is about 80% Jerkass and 20% this. Thing is, boxing happens to be the one thing he happens to take seriously, and therefore takes it very seriously if a boxer disgraces himself or respects a boxer that fights well, regardless of the results of the fight. Aoki and Kimura get especially surprised of him when he approaches Ippo, not to mock him, but to congratulate him after he loses against Date Eiji. He was also extremely brokenhearted after the Mama Bear incident, when he finds out that Nekota had killed the very same bear Takamura spared on account of her cubs, he literally cries. For a guy that beats up his fans and grabs people's cocks in the shower on a regular basis, this shows that he at least has some kind of idea of common sense.
Also Takeshi Sendoh, who is Hot-Blooded and a borderline Blood Knight... but actually started fighting to protect people rather than hurting them in purpose.
Hanaukyō Maid Tai. Konoe, especially in 'La Verite''. She starts off very stern and strict with Taro, but ends up becoming friendly toward him
Domyoji Tsukasa of Hana Yori Dango, who manages to be a sympathetic male lead despite frequently beating up random bystanders for no reason.
The titular character is selfish, bossy and arrogant, but she does treat the Brigade members very well, like after Kyon fell into a coma in Disappearance and when Yuki fell sick because of the Sky Canopy Dominon in Snow Mountain Syndrome. Most recently seen in the end of the beta storyline of Dissociation.
Kyon likely also qualifies for this trope. He's prone to presenting himself as a world weary Deadpan Snarker, but he's a deeply compassionate person who treats everyone equally and seriously in thought, if not in action.
Tomoe from Kamisama Kiss is normally sarcastic, rude and highly critical of just about anything Nanami does. But if anybody else tries to insult her and/or criticize her he is quick to come to her defense and if you hurt or threaten Nanami in any way, shape or form you're in for a world of pain.
In Karneval, Gareki, Hirato and Akari can all be Jerk Asses, considering that Gareki's personality is rather Tsundere and the latter two are rather cold toward people. BUT Gareki obviously has a weak spot for Nai's innocence (though it won't spare the poor kid getting bonked in the head, and all the other annoying brats in the world can go rot for all he cares), Hirato seems to effectively hide how much he cares for his crew and how often he makes certain of Nai's safety, and Akari is harshly vocal about Hirato's apparent callousness toward his crew and the people essentially under his care.
Tanimoto. He acts like a Jerk Ass towards Kenichi, but when push comes to shove, he's willing to throw his lot in with the Shipaku Alliance. He acts like a Jerk Ass towards Kenichi, but when push comes to shove, he's willing to throw his lot in with the Shipaku Alliance.
Nijima also counts; while he seemingly doesn't care about the desires or well being of the Shinpaku Alliance (especially Kenichi), he's shown that his is willing to stick out his own neck for the team when he really needs to.
Akira Hongo, the "God Fist" of YAMI's One Shadow Nine Fists, proves to be this as well. He looks and acts like a very aloof fighter, but over time he is revealed to have been a very good mentor to his now-deceased prize student Sho Kanou (and later, to Kanou's fellow students under him as well), and he didn't take it very well when he learned that Kanou had died at the end of the D of D Tournament arc. It's also indicated that he's always respected the bond between master and student (hence the reason he advises Sakaki to go support Kenichi instead of fighting the Demon Fist, which he does himself) and Kenichi earns his respect for standing up for Kanou's self-sacrifice to protect Miu during the aforementioned D of D.
Giroro of Keroro Gunsou. He's normally a hard-boiled warrior, but he's proven that he's willing to go all out to protect the squad. And even moreso, Natsumi. He also shows his softer side to his cat.
While Pauley Cracker from Kimba the White Lion can be sarcastic and pushy, he cares deeply for his friends and is willing to do what it takes to help them.
Kimi ni Todoke actually has a few examples, but the purest would be Pin, the homeroom teacher who shows little to no sympathy for any of his pupils, goes out of his way to embarrass people and generally just acts really rudely to just about everyone. Despite this, though, some Pet the Dog moments and a couple of occasions on which he actually gave pretty good advice have shown that he's not so bad, deep down.
Alto Saotome from Macross Frontier acts like a jerk to a lot of people and in the beginning mutters about how much he hates his home, Frontier, but in spite of it does everything he can to protect it. He's particularly a Jerk Ass with Sheryl at her teasing, leading to the obvious conclusion.
Chamo. Sure, he's a Dirty Old Man in ermine form, and constantly tries to manipulate people for his own gain... but he never puts his own goals above the safety of the rest of group, tries to make sure everybody else benefits along with him, and generally tries to make himself as useful as possible, even when an ermine generally wouldn't be able to do anything.
Ayaka Yukihiro has her moments as well — when she's not being a spoiledOjou, she shows herself to have strong principles and be genuinely quite caring of others.
Tosaka seems to be like this too. He constantly bullies Ako, and constantly complains about her, Negi, and everyone else, and willingly turns over the evidence that could send Negi to prison at no cost after blackmailing him with it, even though Ako volunteered all of her rights and was willing to essentially become his slave for life. Tosaka also implies that while that is what she might have meant, some rather nastier things may have happened as well if she'd gone through with it. He also tells Negi that his Missing Mom, Arika, was an extraordinary person, and he cherishes the memory of the single time he met her (when Tosaka was a mere Street Urchin) very fondly. And then, he pulls a Heroic Sacrifice, Taking the Bullet for Ako.
Dynamis fits the bill as well. At first he seemed to be an aloof villain, who is completely condescending to Fate's minions, saying what a shame it is that Cosmo Entelecheia has gone from being a massive organization to relying on four little girls to do their dirty work. Then he thanks those same minions for staying with them, because without them it would have been impossible for them to have gotten as far as they have, and that they should be proud of themselves for surpassing the Cosmo Entelecheia of the past. Koyomi even lampshades it.
Oddly, Himari's possessor comes off as this in Mawaru-Penguindrum. This is the same entity that horribly insults a young girl like Ringo all over when summoning her an Shoma to her presence, and some episodes later summons both of them again... to give a Ringo who has just had an Heroic BSOD some space to cry about her huge troubles. While still calling her mean names.
In Medabots, Couch Mountain seems like a cruel man who makes students run laps for no reason, and seems to be doing deals with shady characters. In reality, he was trying to buy land to put up a park for poor children. And then, in the end, he makes the main characters run some more laps for staying up late.
Lead bully Samatha might also be one of these, charitably keeping around her totally incompetent minion Spyke and often helping the heroes out when they really need it. She just does a damn good job at hiding it (and does actually fire Spyke in one episode, though not without provocation).
Hitoyoshi Zenkichi from Medaka Box definitely qualifies, he bitches and moans about having to do things all the time, will chew someone out in a moments notice, gives up constantly and he goes to extreme lengths to show how awesome he is (in one week he tried out every club the school had to offer earning the nickname Bukatsu Storm), but if you even think about doing something to one of his friends he will make sure you go down, even if he has to go down with you.
Mitsuba from Mitsudomoe has a dismissive and superior attitude towards everybody. Yet, she just as often slips up and reveals that there's some genuine kindness in her. One of her earliest examples is the replacement pencil cases Futaba made. Mitsuba kept using hers well after her sisters no longer were.
Toru Muhyo in Muhyo and Roji. While he is typically fairly cold, showing either irritation with or disdain for those around him, he often does this to teach Roji subtle lessons, and typically goes out of his way to get the best possible result for the ghosts he deals with, even when he seems to be taking a harsh stance on them.
Rival Executor Daranimaru Goryo might fit into this trope as well. Although he may appear a ruthless bastard, he actually shows genuine concern for his assistant Ebisu, and even cries over him. Twice.
Murasakiiro No Qualia: Tenjou acts like a jerk towards Yukari but has actually always been doing her best to try to understand her better. This attitude only manifested after the event in their past.
Nadia herself wavers between being a complete Jerk Ass and a Not Good with People sort of person, but in the canonical episodes of the story, she fits into this trope. Aside from being suspicious of other people, she has a nasty, quick temper and gets angry quite easily, misunderstanding everyone's actions at the drop of a hat. That said, she is also shown growing to care for Jean, as evidenced by her attempt to comfort him about his father's death, and even suggesting him to build another aircraft to cheer him up. She even brings him a half-baked dish of seaweed. She's also transformed by the end of the show into a genuinely caring person. She sacrifices her Blue Water's power to resurrect Jean, and even marries him.
Grandis Granva, most definitely, although Sanson and Hanson could both qualify, too.
Captain Nemo. Most of the time he is very reserved and sometimes makes harsh decisions, but he's fundamentally a good person who cares for his crew and mainly wants to stop Gargoyle from destroying the world. He even comes to see Jean as a surrogate son and even has a soft spot for Nadia. It turns out he's her father.
Ban from Nanatsu No Taizai comes up as a jackass who doesn't care about anything but himself and the stuff he steals but in his backstory, when he went after the elixir of immortality, Elaine told him that if he were to take the elixir, the forest surrounding it would die. Ban promptly decided that it wasn't worth it (claiming that the wild berries used in one of his favorite drinks was grown in that forest). He may be a thief, but he is not a monster.
In Part I, the eponymous character was a brash, temperamental brat fond of picking fights with everyone and completely lacking in social graces, but he was also surprisingly kind to people like Inari and one of the few to interact with Gaara as an equal rather than with fear or hate. During the second part of Naruto, however, his previous slightly jerky attitude was downplayed as he matured both emotionally and physically."
Sasuke on the other hand, is a complicated issue. He fed a tied up Naruto during the bell exam. The scene where he saved Naruto's life and told Naruto that it was his duty to save Sakura, where he said he didn't want to lose those important to him doesn't leave any opening for interpretation. He was a Jerk with a Heart of Gold... sadly, the emphasis is on was.
In the recent chapters, he becomes this again when he finally chose to protect the Hidden Leaf Village rather than destroy it.
Sai is also introduced as an abrasive Jerk Ass, but mellows out and turns into one of these after Naruto establishes bonds with him.
Asuka Langley Soryu is incredibly Hot-Blooded and a wicked Tsundere, but despite that, she still tries to be compassionate to Shinji. Unfortunately, he's just too secluded to open up to her, leading to many angry confrontations between the two over his cowardice and her arrogance. Worse, she hates Rei with a passion for her emotionless nature and unnatural talent for piloting an Eva.
Her manga counterpart, as well as her Rebuild counterpart, Asuka Langley Shikinami, are more clear-cut examples of the trope, showcasing and developing better traits on a more frequent basis than in the original anime.
Ryoji Kaji has made a reputation with Misato for being an insensitive, underhanded, and slobbish man. The first trait is caused by a misunderstanding and fades once it's cleared up, while the third seems to be just to tease and spite her. The second, however, is VERY true... and gets provenin the worst possible way.
Magari Kazuma of Nora spends the first two volumes of the series treating the titular Hot-Blooded demon like a misbehaving puppy and most of his classmates like idiots, claiming flatly to make decisions based solely on which outcome will most benefit or least inconvenience him, and being generally bastardly to everyone. And yet... he will do anything to protect the people around him, often foregoing magic and just leaping irrationally to their defense, quite at odds with his normal Magnificent Bastard-in-training persona. And you really don't want to imply that humansareinferior; the results are not pretty.
Nezumi from No. 6. He can be a jerkass at the very least. But he also sings to Dogkeeper's dying pack members to ease their suffering, to say nothing of what he'll do where Shion is concerned.
Roronoa Zoro acts distant and somewhat insensitive to others (and outright insults Sanji a lot of the time), but has shown himself willing to go through Hell and high water for his True Companions, even willing to take on the World Government and all their resources to rescue them. He's had plenty of Pet the Dog moments too. Mostly to do with Chopper or kids.
Nami as well. She originally had to act like a thieving jerk in order to help her village from a ruthless gang lord, but after she was freed from her debt, made it apparent that she was still as greedy and manipulative as ever. She has shown a soft spot for women and children and, thanks to Character Development, even was willing to give up part of her wealth to Rolling Lola out of thanks and later forgave a former member of the gang that had terrorized her village and tried to help him win back a kidnapped mermaid friend with a large part of the wealth collected by the crew.
Smoker did this in one scene, where a little girl with a 3 layer ice-cream cone bumps into him, instead of getting pissed at her for staining his suit, he gives her money to buy a 5 layer ice-cream cone, and apologizes to her.
No mention of what is probably the best example of One Piece? I bring you Curly Dadan, Luffy and Ace's foster mother. She constantly complains about how much of a nuisance Luffy and Ace are, and often treats them not too kindly, but in the end she is very protective of them. She can't even praise them without calling them "idiots" or "assholes".
Harlem from Papuwa fits this trope towards Kotaro and Liquid.
Officer Ohta, Patlabor. He once went to an arranged date, did like the girl quite a lot... and helped her out when he learnt that she was in love with someone else and the guy was in serious trouble.
Drew from the Hoenn arc of Pokémon is like this. He especially loves switching between both halves of this trope when he's interacting with May.
Randou from Pretty Face. The jerk part caused basically everyone he was in contact with to either fear or hate him, except for his crush, who saw the gold part in him. Eventually the gold part becomes more notable.
Kyoko from Puella Magi Madoka Magica. She's very callous and selfish, advocating that magical girls should only use their powers for their own benefit. In her first appearance she would have killed Sayaka if Homura hadn't intervened, but after learning the Awful Truth that magical girls are basically liches, she becomes much less antagonistic. Her heartbreaking backstory makes it clear that when she says magical girls should be selfish, she really is trying to help Sayaka by preventing her from making the same mistakes she did. Her shift away from jerkassitude is made clear when she saves Sayaka from Homura, in an ironic reversal of their first encounter. Her heart of gold becomes especially apparent after Sayaka becomes a witch and she tries to bring her back. This fails, and Kyoko uses a suicide attack on Sayaka so that she won't have to die alone.
Also Akane Tendo, although in her case the proportions might be reversed (i.e. mostly nice, but a real jerk when inclined).
Genma Saotome. While he maybe selfish and abusive towards Ranma, he still cares about his son. In a Crowning Moment of Heartwarming, he gives a young Ranma his blanket when he's cold.
In a couple of recent arcs, Gin from Rosario + Vampire has had some character development that takes him from the Jerk Ass / Handsome Lech territory he's been inhabiting for most of the series to Jerk with a Heart of Gold when he silently takes the fall for an ex-girlfriend inadvertently causing problems on campus. (Implication being that, far from the simple conquests he claims them to be, he still holds feelings for at least some of his exes.) Then he becomes a one-man wrecking crew to take down the Fairy Tale organization because they hit his Berserk Button of messing around with his friends, specifically Sun, the one girl who has gone toe-to-toe with him and gained his respect.
Genjou Sanzo from Saiyuki counts. He makes (empty) death threats at his companions, calls them his servants, and often employs physical violence on them (Paper Fan of Doom with Goku, gunshots with Gojyo that he obviously means to miss because he is a ridiculously good shot) - BUT he rescues Goku and keeps the kid around even though there's no advantage in doing so, argues for leniency on Hakkai's behalf with the Three Aspects and later brusquely reassures Hakkai that indeed yes, he deserves to stay with the group, gives a pep talk veiled in rudeness to Yaone and Dokugakuji during "Against the Stream" so they'd get over their confusion, repeatedly says he won't interfere to help/is not on anyone's side, but then proceeds to do so, often with an excuse. The examples can go on.
Half of the cast of Samurai Deeper Kyo, though some of them are really hidden. Kyo stands out as his Character Development advances, but we also have Bontenmaru (heavy on the heart of gold, light on the jerk), Shinrei, and even Hishigi.
Bad Bird from Samurai Pizza Cats gets into this sometimes. Especially when his childhood friend Carla is around. Guido also fits, though being one of the good guys, he has more "Heart", and a lot less "jerk".
Kiyoshiro from Shattered Angels. He gets better once he sees his brother again and discovers what a monster he really is.
Yuuki Natsuno in Shiki is a bit cold and distant towards others not to mention he hates the village helives in, but when a vampire attack occurs he isn't afraid to put his life on the line to stop them.
Zelgadis of the Slayers franchise, namely the anime, is definitely this; he's cold, arrogant, and even haughty at times, but he just wants to be human again, truly cares for his companions, and has a soft spot for the princess Amelia. In the original novels, though, he is more of a straight-up Jerk Ass.
The novel-exclusive character Luke is also this trope, almost identically fitting it the way Zelgadis does.
In an odd main character variation, Sara Werec of Soukou No Strain. The difference is, we already know how good of a person she is, and how she's put away her kind and friendly nature because she blames herself for her dead schoolmates and just wants to stopher brother. The Space Squadron, however, does not.
In Soul Eater, Soul and Black Star border on this at times, as Black Star often seems so full of himself he hardly has time to care about anyone else, and Soul is usually the Deadpan Snarker that appears to only really care about advancing himself at times. However, both care about their friends and partners, with Black Star willing to "share the stage" with Tsubaki, while Soul regularly protects Maka from harm.
Don't forget Mifune, who is one of the best swordsmen in the world and regularly faces off against Black Star, yet carries around candies for children and swings his sword for a small child witch named Angela.
In a way, Black Star's treatment of Crona could be seen as this. While he fights in the only way he knows how, brute force, he does make his own kind of attempt to get through to Crona by insisting that Crona could have someone to rely on in him, the one around whom the world revolves (or something to that effect). And then there's Black Star having Angela come to Shibusen, as Sid did for him.
Stein could be seen as a particularly creepy example. On the one hand, his violent tendencies are disturbing when not played for laughs, on the other it becomes clear over time that he does care about others to some extent.
Manabizaki from SWOT is more concerned with studying than with people. He insults people and treats everyone as beneath him since he has "the greatest brain in the universe." Or, at least, he claims not to care. He's come to the rescue of a wimpy male classmate (later a friend) more than once and an ex-delinquent girl he's developed a crush on. His sputtered and obvious excuse? The people attacking them were making too much noise for him too study. Or he was just on the way to a test/class/study-session and the guys were in the way.
Asada from Team Medical Dragon frequently acts like a misogynistic, perverted, carefree Jerkass. Then a patient gets in with an improbable injury, he saves the day and proceeds to lecture everyone about how the patients' well-being is the most sacred priority. And he's totally incorruptible.
Don't forget Ataru Moroboshi of Urusei Yatsura, who combines this with being a Casanova Wannabe. It's strongly hinted that the reason Lum loves him so much is because she can see the noble parts of him that most others (including himself) can't.
Hamel, the titular Violinist of Hameln (manga continuity only). He purposely humiliates people, charges exorbitant prices for anyone who hears his music, plans zany schemes to make money, actually uses his friends as ammunition and is so selfish he'd rather eat his crow companion than go hungry for even a little while. And believe it or not, he really is a good guy underneath it all.
Sawamura Takeshi in Wa ga na wa Umishi seems to be this, but only because the main character Rintarou rubs him the wrong way. He's not above hitting and threatening Rin frequently, but he's also saved Rin's life more than once. Whenever there's a job to be done he's the man to do it.
Tsume from Wolf's Rain. Always acts tough and cynical and frequently argues with the other wolves, especially Kiba, but is often protective of them, especially the younger wolf Toboe who idolizes him.
Also to some extent the human Quent. When he's not obsessed with wolf-hunting he can be a fairly decent guy, if you buy him a drink.
Seto Kaiba and Katsuya Jounouchi from Yu-Gi-Oh! Kaiba has emphasis on the jerk part, Jounouchi on the heart of gold one.
Yusuke Urameshi and Kazuma Kuwabara, YuYu Hakusho. Hiei goes beyond this and all the way to Noble Demon. Yusuke REALLY embodies this trope. He's a street fighter, a teenage punk, and generally has an extremely negative outlook on life. He lacks any basic manners of a basic human being, but he really cannot stand those who hurt the innocent. He's also EXTREMELY overprotective of his friends, particularly Keiko.
Megumi of Servant × Service tends to frequently verbally bitchslap everyone, particularly Hasebe and Ichimiya. On the other hand, she's shown to be quite the Cool Big Sis figure for Touko, and generally gives Lucy advice that is actually sound in context. She also goes out of her way to help save Hasebe and Lucy's relationship.