Marley, a country outside the Walls that's Putting on the Reich, turns a group of Tyke Bombs into anti-villains by virtue of convincing them that Eldians, people like themselves with the power to turn into Titans, are all devils who committed monstrous atrocities in the past and the people of the Walls are both the worst of the bunch and a looming threat to the entire world. The kids are indoctrinated to believe they must atone for their ancestors' sins by leading a mission into the Walls to destroy the population there. On a personal level, several are also seeking to gain honorary citizenship status with Marley so their families can live lives outside the ghettoes.
While all the Titan Shifters who infiltrated the walls have issues developing from how long they spent among the inhabitants, the Armored Titan, Reiner Braun, has it the worst. He was a tried and true patriot who wanted to earn citizenship so he and his mother could be reunited with his long lost father. He endures a Trauma Conga Line in which his Marleyan father wants nothing to do with his mixed-blood son, he learns he wasn't the originally intended recipient of the Armored Titan, and the one who caused to be him gets eaten before he can explain anything else. He's driven to continue the mission, no matter what, by a mix of patriotism, family, and a desire to not see the effort thus far go to waste, and it breaks him. In adulthood, when he's confronted by someone who has every reason to hate him, the other party explains that he's actually come to understand what drove him, that he was, in his own way, trying to save humanity.
After the Armored Titan returns home, the story focuses on him at home and we see as he has to watch a whole new generation of children being trained to become inheritors to the Titans, including his own when his lifespan, shortened drastically by taking on a Titan power, reaches its end. The children are clearly every bit as indoctrinated as the generation before them was, as they see no problem with being utilized as Child Soldiers even without having Titan powers.
Berserk owns two examples: Rosine, a female Apostle who looks like a pretty moth-fairy, and Sonia, a cute blonde teenage girl who is nothing short of the Big Bad's PR and messenger.
Starrk is Captain Kyoraku Shunsui's barely Evil Counterpart. His list of evil acts include snatching Orihime away from Ichigo and returning her to Las Noches' fifth tower, and lazily fighting against Kyoraku (and Ukitake, Love and Rose). He never actually hurts Orihime and flat-out says that he's only doing this because Aizen ordered him to, and offered to pretend-fight Kyoraku because he's just that damn lazy. The only reason this guy is evil is because he's an arrancar who works for Aizen.
His status as an Anti-Villain is finally driven home when his motivation is revealed. He fights for Aizen out of gratitude to him for ending his loneliness, but even then, doesn't ever want to fight seriously. Then, when he finally does decide to get serious, his motivation for doing so is Lilynette pointing out that fighting for real is the only possible way to stop more of his True Companions from dying.
Also from the Espada, Tier Harribel. Cool, calm, and collected, and the only reason she's fighting is loyalty to Aizen. The only times she shows any emotion is when her subordinates get incinerated by the Commander-General and when Aizen betrays her.
From the Shinigami, there's Tousen, who left Soul Society because of a Karma Houdini towards a murder committed there, and Gin, whose Morality Pet is Rangiku.
From the Bount Filler arc, Koga Go only sticks with the Bounts because of his loyalty to Kariya, loyalty that ends up backfiring on him when Kariya turns on him. And Maki Ichinose only wants to avenge his former captain, who was killed, and eventually undergoes a bit of a Heel–Face Turn.
In the anime Blue Seed, nature God, Lord Susano-oh, is immediately described as the Big Bad that wants to destroy the human race, so that his plants the Aragami can rule and dominate. Turns out that's not true at all. Susano-oh doesn't hate nor want to destroy the human race. He doesn't even control the Aragami. Their controlled the by series true Big Bad, Murakumo. He just wants to return the planet back to its rich natural origins, before the dangers of technology and industry destroy the planet for good. Which is why Kaede agrees to side with him and help him achieve his goals.
Mikuni of [C] - Control is a strong and wealthy man who felt that he could used the midas money to help Japan by buying all of Japan's debt. He was kind to Kimiminaro and wanted to mentor him. He has a different philosophy to money than Kiminaro. However, he may have made things worse by underestimating the Financial District's powers and made things worse in Japan.
Suzaku Kururugi . Despite working for The Empire, he is, in some ways, more 'heroic' than the show's protagonist.
In fact, nearly all of the show's "villains" fit this trope. The aforementioned Suzaku is actively working to reform Brittania from the inside (or so he claimed early on, only for it to be revealed as a cover for a death wish) during the first season (in the second, he simply chose to work for Britannia so he could gain Area 11 as his own territory), most of the Knights of the Round are affablePunchclock Villains, Gottwald's sympathetic backstory mostly makes up for his misdeeds in the service of the empire (which are rendered moot after his Heel–Face Turn), the only completely evil villains were Psycho for Hire Luciano Bradley, Emperor Charles zi Britannia, and V.V.
Even Charles and V.V. and Marianne could be considered anti-villain as all they wanted was to kill God to create a world without lies and equal. This desire was born from being raised in the Big, Screwed-Up Family that is the Britannian Royal family where their mother was killed in front of them when they were no more than 10 years old and only because they were appointed heirs to the empire.
Schneizel's kind of an odd case, perhaps showing the difference between being Affably Evil and an Anti-Villain. He's pretty nice for a villain and Cornelia's comment when he spares her life could be read as Word of God calling him an anti-villain, but hisUtopia Justifies the Means plan is certainly more evil and selfish than Lelouch's is and isn't much better than his father's plan.
Schneizel is perfectly willing to throw his minions away, especially during the Damocles arc, when he attempts to abandon Nunnally and the entire personnel of the rigged-to-explode station to save his own skin. Lelouch, in contrast, tries to make people follow him out of their own free will, even former enemies who regularly battled against him before.
Except when he doesn't. He doesn't seem to have that much of a problem tampering with people's wills to get what he wants.
Mello from Death Note puts aside his rivalries to play a pivotal role in ending the greatest ever reign of terror by a mass murderer playing God. It just so happens that he plays this role by kidnapping, shooting people down (or having others do it for him), and blowing some stuff up, all while working with the Mafia. But it's for the greater good, really! ...And, you know, that raging inferiority complex.
Enpi-chan in the re-make of Dororon Enma-kun is the older sister of the main character, and is the one who helped bring demons into the human world to cause mischief. But she's only doing so with the vague goal of making the world a more fun and sexy place and was made to think that this was the way to do it indirectly by Heaven, and more often than not, ends up in an Enemy Mine situation with the heroes when her minions go against that goal.
Fat Majin Buu. He kills people and destroys cities, but only because he has a childlike mind and doesn't really comprehend that it's wrong since that's all his creators ever taught him to do. When he eventually makes a friend who explains to him that it's bad, he stops.
Androids #17 and #18 from the main timeline are not only stronger than their other counterparts from the different timelines, they are also not nearly as malicious as them. The only reason why they chase Goku they think it's like a game and they don't actually try to kill the Z Fighters, they even spare their lives. It's also shown (in the manga and in filler scenes) that they don't seriously harm other people.
Android #16 even more so. The only evil thing about him is his programmed goal of killing Goku. Besides this, #16 is a Friend to All Living Things, he doesn't like fighting, and he fights only Cell during his entire life because Cell is a threat to his friends and to the nature.
Whis is a really decent guy and probably would be a heroic character if he didn't happen to be a Battle Butlerand all-powerful mentor for a Jerkass God. Later on when the Z-Fighters have earned Beerus' respect, Whis becomes something of a Big Good, using his magic powers to help the good guys like reversing time to stop Frieza's Rage Quit from destroying the Earth.
In Eureka Seven, Dominic hardly qualifies as a real villain at all straight from the start. He sides against Gekkostate for most of the series, but he's generally a fairly nice and harmless guy. Similarly, Ray and Charles Beams are some of the nicest, most loving people Renton meets in the entire series. Unfortunately, their connections to the military along with a personal grudge against Eureka make them enemies of the protagonists. Anemone also moves toward being an Anti-Villain as the series goes on and we discover more of her true personality and tragic past.
Fairy Tail: More than half of the bad guys are sympathetic to a degree. (See the YMMV page for Type IVs)
Type I: Kageyama (dark guild member, but can't commit a mass murder when given the chance), Azuma.
Type II: Juvia before her Heel–Face Turn, Jellal (who is also a Type III), The Oración Seis Except Brain, Ultear and Merudy.
Type III: Reitei Lyon and his group, Laxus, Knightwalker, Hades.
The Black Lotus organization of the Justice/Vengeance chapters of Franken Fran are out to destroy the world! ...by running orphanages, settling disputes, and providing free care, so that mankind will suffer from overpopulation and wipe itself out. Their leader is also very much concerned about his minion's well-being.
Greed and his chimera henchmen. He even eventually bleeds into Anti-Hero later on.
Scar also fills this role to those who don't believe him an Anti-Hero. Most of the people Scar kills are shown to be unrepentant war criminals or mooks belonging to the government, which had them commit genocide alongside the war criminals, and a pair killed during a major BSOD during the genocidal war. Even Scar himself admits that he doesn't deserve redemption.
Fullmetal Alchemist: Brotherhood gives us Isaac the Ice Alchemist. He goes out trying to kill King Bradley due to his disgust over the Ishvalan Massacre. And considering what's revealed later in the series, if he had shown up later on, he probably would've been allied with the heroes.
Among the Homunculi, Gluttony and the aforementioned Greed are the best examples, while Sloth's a pretty good example of a Punch-Clock Villain. Although the other four are undeniably cruel, all of them have some sympathetic quality or another: Bradley is Wrath in this one and despite still being a bastard, is less sadistic and almost comes to admire his human adversaries; Lust seems to have genuine care for Gluttony and Envy, plus loyalty to Father. Envy & Pride, meanwhile, have pitiful traits despite their sociopathy - the former actually envies humans for all their good qualities and because it can't emulate them, can't help but hate them; the latter follows his Father's teachings to the letter, and only upon his (near) death realises that Father never cared for him in return, and his adoptive human mother was the one person who truly loved him (it's shown that when she raises him from scratch, he becomes a genuinely kind-hearted child). Actually calling any of these four an Anti-Villain is a stretch, however.
Aoi from Ghost in the Shell: Stand Alone Complex is a young hacker who wants to expose the government coverup of a cure for "cyberbrain sclerosis", an degenerative mental disorder that afflicts some people who have had their brains cyberized.
Kuze in the second season. He tries to assassinate the prime minister, is part of a terrorist group, and attempts to arm the refugees with nuclear weapons. But it turns out that he only did it because he seemed to be the only one who really cared about the desperate situation of the millions of homeless refugees in east Asia, and tried to do at least something about it. Having a very tragic backstory only helps solidify his place as this.
Initially, he was set up by Gohda's hero-producing virus as well.
Garma's older brother Dozle deserves a mention, too. In spite of serving the country that instigated the war, he is probably the most likable Zabi. He cares about his soldiers, and would sacrifice his own life making the last stand alone in Solomon to get the surviving Zeon soldiers and his family to safety.
Gundam Wing has Treize Kushrenada, who wants to unite the world and bring peace to it by giving it a war so spectacular and horrible that the people will cringe at the thought of another one. To do so, he's willing to go to any ends, such as manipulating people, assassinating political opponents, and launching vast conquests. But he's also one of the most noble characters in the series, who acknowledges full well his atrocities, and remembers the name of every single person who died because of him as a memorial to them. He even intends to die in what he perceives to be the final battle as atonement.
Gundam 00 has several, mostly because the protagonists' goals (uniting the world as one) conflict with a variety of not-evil interests in the current politics. The most notable is Colonel Sergei Smirnov, who's generally regarded as the most honorable, moral, and downright ''nice'' person in the entire series. It's considered telling that he's the only antagonist character thus far that hasn't wound up in the Titans homage organization A-LAWS (though Kati Mannequin only joined at his request because someone needed to keep an eye on such a secretive and powerful organization. Also, loser ace Patrick only joined because he's got a crush on Kati, despite her telling him not to do so).
Gundam AGE has Zeheart Galette in the second generation. During his infiltration mission as a New Transfer Student, he forms genuine friendships with the people around him, especially future Gundam pilot Asemu Asuno. He's deeply troubled by Asemu's determination to be a soldier because he doesn't want a kind-hearted person to end up like him, and tries several times to persuade him not to be a Gundam pilot for that reason (and because Asemu's presence on the battlefield interferes with Zeheart's judgment). He's also willing to sacrifice himself to stop a space fortress from crashing into Earth; fortunately his boss Lord Ezelcant saves him.
Iron-Blooded Orphans has Gaelio Bauduin, a kind-hearted person who believes in justice but works for Gjallarhorn, the Gundam-standard oppressive Earth government. He doesn't do anything more villainous than engaging in some very mild anti-Martian racism and anti-transhumanism, but those attitudes seem pretty institutionalized in this setting. On the flipside, he expresses disgust when his superiors use a False Flag Operation to slaughter rebellious colonists. Then near the end of the first season he goes through a Trauma Conga Line, losing friends left and right before being literally and metaphorically back-stabbed by his supposed best friend McGillis Fareed, apparently dying in the process.
The second season gives us Gaelio once more, this time using the Char Clone identity "Vidar". Despite everything he's been through he's still generally a noble person, apologizing to Mikazuki for looking down on him the last time they met and defusing proto-Tyke Bomb Julietta by leading her towards his more idealistic way of thinking rather than the darker path that others (like her commander/idol Rustal Elion) seem to be pushing her towards. Mostly he just wants revenge on McGillis for all the damage he's done, and though he gets it it turns out to be utterly hollow and he actually finds himself sympathizing with his former friend as he dies. By the end of the series, Gaelio is one of the few characters who never engaged in any morally questionable actions, which considering the setting is saying something.
Haruhi Suzumiya: At least two members of the Anti-SOS Brigade are this trope. I say "at least" because, though Fujiwara is probably the most traditionally evil character in the series, his ultimate goals are actually pretty noble, due to Fridge Logic, and Kuyou's motivations are completely unknown at this point. The ones who are pretty surely Anti Villains, however, are Kyouko, who prefers not to use violent means to achieve her goal (which, if realized, would make the world more stable, though less interesting), and Sasaki, who wants nothing whatsoever to do with the supernatural, and is only involved in the plot because the aforementioned Anti-SOS Brigade just will not leave her alone.
Koga the Wolf Demon is treated as The Rival, constantly arguing and bickering with the eponymous Half-Human Hybrid over various topics, including his own desire to wed Kagome and kill Naraku for the death of his whole tribe, and most of the lesser wolves that followed them. The group seems to have forgotten that Koga, before Kagome helped save his tribe from the Birds of Paradise, once slaughtered several nameless villages just to feed his wolves and kidnapped Kagome in the first place because he intended to use her ability to see Shikon shards for his own ends.
Kagura, wanting her independence from Naraku, having a tendency to Pet the Dog, especially when it's Kohaku, and giving her life to protect Kohaku.
Sesshomaru oscillates between this and Anti-Hero while slowly but eventually defrosting throughout the series.
Toyohiro Kanedaichi in Part 4 is a guy who's trapped by Superfly, an autonomous stand bound to an abandoned transmission tower that requires one person to be inside of it at all times. The only reason he fights with Josuke at all is because he desperately wants to escape by trapping him inside it instead, and even when he thinks he's about to get away he offers advice to Josuke so he can get out later. After enough fighting, Toyohiro realizes that he's been trapped for so long that the outside world is actually kind of scary to him, and since he's already made a comfortable living inside the tower he decides to stay.
La Squadra di Esecuzione in Part 5. A great deal of them, especially Nero and Pesche have humanizing traits of True Companions-ship despite being the enemies of the heroes, as well as their need for vengeance against the Big Bad for killing their two friends. They still want the money of the drug trade, mind you.
Any non-Maniwani villain in Katanagatari, and you could include the Maniwa Insect Squad. Their motivations earn some sympathy, even if they did betray Togame, most especially Tsuruga Meisai and her turning that shrine she's in into a refuge and using the swords she got to protect its residents.
From Ragnarok, Takeda and Thor are portrayed as anti-villains essentially from their introductions. Ukita becomes one in the brief interval between turning against Ragnarok and actually allying with Kenichi. Kisara becomes one basically as soon as we see her taking care of a stray cat. Freya and Siegfried show their non-villainous sides in their main fights against the protagonists. Even Berserker shows some signs of anti-villainy: he has no evil goals, he's just a Blood Knight and is very easily bored. Both Berserker and Odin become outright anti-villains in later arcs.
From YOMI, Raichi and Ethan are Friendly EnemyPunch Clock Villains. It's explicit that they would be friends with Kenichi if they weren't on the Other Side (Raichi even has a Villainous Crush on him!). Boris and Rachel are both also Punch Clock Villains, and develop into anti-villains following their failures to kill Kenichi. Chikage and Rimi are implicit anti-villains to varying degrees: Chikage is only villainous in "Yami mode" and Rimi is really driven to villainous actions out of a desire to prove to Ryuuto that she is "strong". Ultimately, all unarmed YOMI members (except for Kano Sho who is dead, Radin Tidat Jihan, Ryuto Asamiya, and Rimi Kokorone who are no longer members, and Kajima Satomi and Li Raichi who are not present (assuing the Li family is still associated with Yami; it's unclear) pull a collective Heel–Face Turn and aid Shinpaku Alliance against armed YOMI.
Even Yami itself is bristling with anti-villains. Agaard, Rahman, and Hongo are all kind, friendly, and heroic to varying degrees, just on the Satsujinken side of things. Diego Carlo and Alexander Gaidar are both shown to have standards and care for their disciples. All of five of the above plus Sogetsu Ma turn against Yami in the end.
In Kill la Kill, it's eventually revealed that Satsuki Kiryuin is one of these. The entire point of her ultra-militaristic and fascist academy and her plan to take over all of Japan is to build an army capable of standing up to her mother, who plans to Take Over the World and turn the human race into food for the Life Fibers. Even her deliberate antagonizing of Ryuko is to toughen her up to be a Worthy Opponent for her mother. Once the cat's out of the bag (and her academy is taken over,) she switches sides and becomes an Anti-Hero instead.
Takarada could count as one. He's greedy and obsessed with money, and perfectly willing to use citizens' greed to recruit them into his army and even burn down all of Osaka during his fight with the Academy. On the other hand, he's still driving Osaka's entire economy, the aforementioned fight is in self-defense when the Academy tries to invade the city, and he states that he'll just pay everyone to rebuild their city afterwards (and none of said citizens really seem to care, anyway.) That's not even getting into the fact that he and his family are secretly funding Nudist Beach.
The Power Trio is told that High Priest Zagato kidnapped Princess Emeraude, causing untold damage to the magical world of Cephiro, so the Knights must defeat him. It turns out, Emeraude imprisoned herself in an attempt to forget about her love for Zagato, since it was making her unable to pray only and completely for Cephiro, which was the thing causing destruction. Since she can't forget him, she summons the Magic Knights to kill her, so Zagato decided he had to kill them since he'd rather have Emeraude alive than Cephiro. Zagato's minions, apart from Alcyone, are Anti Villains themselves; Ascot and Caldina even promise to leave the girls alone after being defeated.
In Magic Knight Rayearth II, the leaders invading countries all have their own motivations. Eagle of Autozam wants to become Pillar because his world is dying from pollution. Tarta and Tatra want to expand Chizeta's miniscule territory for the comfort of their people and say they don't want to oppress anyone. Aska desires Cephiro purely out of avarice, but she's a child and isn't acting maliciously. In the anime, even Nova is given sympathetic reasons for why she is who she is (she is the embodiment of Hikaru's negative feelings, making her a sort-of Superpowered Evil Side), thus leaving Debonair (and Alcyone, as long as she's Brainwashed and Crazy) as the only truly evil villain.
In the manga, Eagle's motivations are different, but they only cement his Anti-Villain status more: he wants to become the Pillar of Cephiro, find another place to house Cephiro's people, and make the land sleep with him when he succumbs to his incurable disease. He only wants to do that because he knows Lantis is going to try to destroy the Pillar System and may very well lose his life in the attempt.
Fate from Season 1, the Wolkenritter from Season 2, and Zest from Season 3 of Magical Girl Lyrical Nanoha. Their "villainous" goals range from wanting to see their mother smile to saving an innocent Ill Girl from certain death to uncovering the truth behind the deaths of their comrades. All of them fall under the Worthy Opponent type, doing things like holding back to not kill people, and going out of their way to make sure their opponent is okay after she's been attacked by a third party. Scenes of them not in battle portray them as genuinely kind characters that deeply care for their wards and those around them. Almost all of them join the heroes' side after being befriended by Nanoha or her cohorts. In fact, a good portion of Nanoha's current cast is made up of former anti-villains.
Other Anti-Villains were Arf (Fate's Familiar), Reinforce Eins who was the Book of Darkness/Tome of Night Sky herself, Gil Graham and his two Familiars, Zest's group (Agito, and Lutecia with Garyu), and the most of Numbers except Due and Quattro; Tre is shown to be not really malicious, she's just loyal to Scaglietti, Sette is in jail because she's loyal to Tre, while Uno is debatable. All other Numbers rehabilated and joined the good characters and they never had evil intentions.
In The Gears of Destiny, the three Materials and the independent Big Bad Unbreakable Dark are all Anti-Villains. Stern and Levi are actually very friendly and are the Morality Chains to their king Dearche, who would destroy the world if she wants, but her two retainers keep her from doing do that because they care about Nanoha, Fate, Signum, Reinforce and the others. The three Materials eventually turn into Anti-Heroines when the story progresses. Unbreakable Dark is a Person of Mass Destruction who cannot control herself and she is forced to destroy anything and anyone she encounters, but she always warns the people to leave her alone, so she wouldn't kill them.
Kyrie Florian from The Gears of Destiny borders between this and Anti-Hero, but she fights the heroes more often than she fights the villains, but not because of misunderstandings like her older sister Amitie, she just do this to finally obtain Unbreakable Dark's vital core, the Examia, which could save her homeworld. Not to mention that she joins the villains at the end of the first chapter to help them revive the Big Bad.
Chao Lingshen will not hurt anyone except The Hero himself. Her motive is to end The Masquerade, which Negi and the rest of the protagonists can't really find any problem with. Negi's only really fighting her because he'll get turned into an ermine otherwise. He actually angsts quite a bit about this, but eventually realizes that if she had a reason for revealing The Masquerade that would justify his being turned into an ermine, she'd have told him already.
Also, Evangeline, who started out as a full villain, but Heel Face Turned early on and is now more of an Anti-Hero than anything. It's later revealed that, even in her depowered form, Eva is still extremely dangerous and could have kicked Negi's ass easily if she had been serious, so she may have been an Anti-Villain from the beginning. Later on, it's implied that a lot of Eva's Uber-Evil reputation is greatly exaggerated, and that what evil she did do was in response to being an outcast in society.
Even Fate is pushed into this corner. One of his past heinous acts? A hobby of rescuing war orphans and giving them free educations. He even sarcastically lampshades it. 'No, I'm a VILLAIN!' read: Because I couldn't have done it because I'm not a total asshole, right? There are also a number of hints that he's an Artificial Human that may have limited autonomy, being programmed to follow the orders of his master. Even his "evil plan" turns out to be somewhat sympathetic. The magical world is going to evaporate soon, taking most of its inhabitants with it and killing the rest. His "evil plan" is to save them by sending them all to a (suspiciously afterlife-like) pocket dimension before that can happen, since most of them can't exist on Earth, and the remaining ones are still too numerous for Earth to handle.
My Hero Academia: Hero-Killer Stain is a vicious murderer that targets heroes that he feels are acting only in their self-interest because he idolizes "real" heroes (i.e. Those who act selflessly and for the sake of right as opposed to for fortune or fame) such as All Might.
Haku was more of a sympathetic Punch-Clock Villain than a true evil menace. Itachi turns out to be this as well, revealed post-mortem; coincidentally, he was paired with Kisame, another character who could be considered an anti-villain.
To clarify, Itachi's actions shouldn't be overlooked as well. The only reason why he massacred his clan and joined the Akatsuki is to protect both Konoha and his younger brother, Sasuke.
Kimimaro of the Sound Five, being something of an Expy of Haku—like Haku, he followed his master because his sad backstory caused him to develop a complete lack of self-worth outside of this role (though unlike Haku's master, Kimimaro's didn't care for him in the least). He was even a deeply honourable combatant, stopping the battle with Rock Lee to allow him to take his medication. If Orochimaru hadn't gotten to him first, he could've been a good guy.
Nagato/Pain turns out to be one of these, along with his childhood friend, Konan.
He's also a variation. Unlike most other Anti Villains, who feel that they can be sympathized and want to redeem themselves, Nagato knows that he can't be redeemed and doesn't want sympathy to begin with. However, his sympathetic backstory and why he did what he had to do put him squarely into this trope.
Sasuke Uchiha becomes this in Part II—though in a variation, he's been steadily Jumping Off the Slippery Slope as time goes by, and one of Naruto's main goals in the story is to redeem him before his Freudian Excuse stops being valid justification for some of the shit he's been pulling (and planning).
Noir's Big Bad, Altena, is a very sympathetic villain; she is shown to genuinely love The Rival, Chloe, as well as having a Dark and Troubled Past involving orphanhood and rape. Somehow, this makes her more creepy.
It's the way she's extremely sincere about her ideals. Sincere enough to be perfectly willing to sacrifice everything that she cares about to fulfill them. Human life seems to have zero value for her, and that includes her own.
There are characters such as Vice-Admiral Garp (who was willing to let Luffy get off scot free until he was ordered to go after him), Koby and Helmeppo (who are both friends with the Straw-hats when off-duty), Admiral Aokiji (who helped Robin escape from the Buster Call on Ohara and managed to get a bunch of the Straw Hats' allies off the hook for helping in the attack against Enies Lobby), Commodore Smoker (who refused to take the credit for defeating the villain that Luffy defeated) and Ensign Tashigi (held off enemies while Luffy was kicking said villain's ass).
Bartholomew Kuma. He's actually one of Dragon's Revolutionaries, working as one of the Shichibukai for unknown reasons. His splitting of the Straw Hats was actually him saving them.
Dracule Mihawk. After his duel with Zoro, he spares him so that Zoro will become stronger and challenge him. As of Chapter 597, he's actually become Zoro's master!
The G8 filler arc has Commander Johnathan, who, other than being a very cunning Magnificent Bastard, seems like a pretty cool guy, and is just doing his job in trying to keep a bunch of pirates from escaping his base. He even gets in a bit of semi-friendly banter with Luffy on a couple of occasions.
Magellan, the main antagonist of the Impel Down arc is like this. He may run one of the worst Hellhole Prisons in fiction, but he is presented as a guardian who honestly wants to prevent all the worst criminals in the world from terrorizing the public. While he is willing to take advantage of the right given to him by the World Government to kill the prisoners if he must, he is much less evil than many other staff of the prison who have that right, and after the mass breakout, he willingly takes complete responsibility for what happened, even at one point considering suicide for his failure. (He does not, and is later simply demoted.)
The Pokémon Adventures manga has two of these, and they aren't played for laughs. Giovanni is the first, as he eventually only wants to find his son, and, of all people, The Mask of Ice, AKA Pryce. This man actually lies about thinking of Pokémon as weapons, and practically screams at Gold that Pokémon are beings to be loved. His plan was meant to bring back his Lapras. And during the flashback of Blue and Silver's escape, an ice sculpture made by him is shown with him and the kidnapped kids together, maskless and happy. You can't help but feel at least a tad sympathetic towards the guy, despite the dog-kicking he did.
N is like this in the Black and White arc of Adventures, even more so than in the games.
Ashram from Record of Lodoss War starts out as one of King Beld's two Dragons, and his first defining scene is the brutal massacre of a keep the heroes are staying at for the night. However, the second series in particular shows him doing everything he does to improve the life of the people of Marmo, so they no longer have to rely on war and pillaging as their only means of survival. He even gains the loyalty of a priest of the God of War, who was awed by his display of all the traits that make a true, honorable knight and defender of the weak.
Rurouni Kenshin gives us Amakusa Shougo. He wanted to take over Japan, destroy the Meiji government, and establish himself as a god-king, to avenge his parents (who, along with many Japanese Christians, were killed off towards the end of the Tokugawa regime.) He wanted to create a new society where his followers from Shimabara could worship as they chose, without being oppressed or persecuted for it, and he established schools, orphanages, and hospitals in Shimabara, and brought some knowledge of Western medicine with him from his travels.
At least half of the twelve Gold Saints are like this during the Sanctuary Arc. Only two of them are actual villains (Deathmask and Aphrodite), one of them is dead (Aiolos), another is Brainwashed and Crazy (Aiolia), another is retired (Dohko), and the Big Bad (Saga)is suffering from a bad case of Split-Personality Takeover. The rest are honestly trying to protect Athena's Sanctuary from what they believe to be evil foes (Shura, Aldebaran, Milo, Camus, to some degree, and Shaka) or actually do help the Five-Man Band directly (Mu). For the most part, once they realize Seiya & Co. are fighting on behalf of Athena, they immediately turn to their side; those who continue to fight do it only because they want to test the heroes' mettle.
Some of the Ansgard saints fit the bill as well; especially Thor, Siegfried, Mime, and, maybe, Sid and Bud. The only one without any likeable qualities was Alberich, and the rest are more selfish or cynical without reaching irredeemable extremes (Hagen, Phenrir).
While the "heroes" are definitely anti-heroes, the "villain" Kougaji of Saiyuki definitely fulfills this role. He's loyal, responsible, idealistic, kind, and generous, even saving his enemies' little pet dragon from dying of thirst. The only reason he's a "bad guy" is because he's being blackmailed into it. His henchmen are similarly anti-villainous.
Hishigi of Samurai Deeper Kyo. He is completely apathetic about fighting for the Aka no Ou, and only continues to do so for his friend, Fubuki.
The eponymous character from Shinryaku! Ika Musume is a Villain Protagonist squid girl who hates humanity and plans to take over the world because they pollute the sea. Considering she's the only squid person around, we can assume that, although she never actually says so, she lost quite a few loved ones. Played with because she's completely ineffectual, doesn't know anything about humanity, and has no idea how to reach that goal or what to do if she actually managed to.
Mifune from Soul Eater is an antagonist and Black Star's biggest rival for much of the series. However, he's really only fighting to protect Angela, a young witch who can't defend herself. He also has a soft spot for children in general, refusing to fight seriously with Black Star at first. Because Angela happens to be a witch, Mifune believes that she will never be accepted by Shibusen and is forced to side with the villains by default. In the anime, his opinion is eventually changed and he is offered a position as a teacher at Shibusen. In the manga, however, he eventually dies in his final fight with Black Star. This is especially tragic, as Angela is taken in by Shibusen afterwards, proving Mifune's entire goal to have been misguided.
Lunatic from Tiger & Bunny a vigilante who specializes in killing criminals instead of capturing them and is willing to kill anyone who gets in the way of his stringent view of justice. However, most of the criminals he executes are truly evil people, he goes out of his way to avoid endangering innocents and other heroes unless they flat out refuse to get out of his way, and, most importantly, he does thorough research on his targets and, if he believes someone has been Wrongly Accused, will actually defend them from police and other heroes. He also has a very sympathetic backstory. When he was a child and his father, Mr. Legend, lost his powers, Legend became a brutal Domestic Abuser. It eventually reached the point where Lunatic was forced to use his own powers to kill his father to save his mother's life. Ever since then, despite taking care of her well into adulthood, his mother still holds him responsible for the event.
Toward the Terra features Keith Anyan, who is almost as much a secondary protagonist as an antagonist. The ending hinges on Keith's Heel–Face Turn as much as or more than it does on any actions taken by the hero.
In the US and Japanese versions of Ultimate Teacher, Ganpachi falls to this, as his goal was to get the school back in shape (though exactly how good of a teacher he would have been is another matter), and most of his methods in the start were crushing to his opponents but not violent.
Folken Fanel from The Vision of Escaflowne. Long, long before his abandonment of the Zaibach Empire and Heroic Sacrifice seems to be even a faint possibility, he's set up as a compassionate, thoughtful man who only performs ruthless acts and atrocities for the Empire because he believes they'll eventually lead to a greater good.
Darcia III from Wolf's Rain starts off as this. He tries to bring Cheza with him to heal his catatonic lover, Hamona, but he does so by attacking her friends and is willing to stop them from reaching Paradise with her. However, when he returns to find Hamona killed by her jealous twin sister, everything goes downhill and he transforms into a full villain.
Though the manga's still on hiatus, Fuuma from X1999 appears to be one of these, and may, in fact, be the only character in the series with any idea of what's really going on, and often strongly hints that the reason he does everything he does is to force Kamui into realizing his true wish, which is the only way that the future can be altered. The anime series and The Movie turn him into much more of an outright villain.
The same can be said of the Dragons of Earth in general, with some of its members not being very villainous at all. The series intended to blur the line between hero and villain.
In Yu-Gi-Oh! 5D's, there exists a group called Yiliaster, which is revealed to be from the future. They are trying to destroy Neo Domino City, but only to Set Right What Once Went Wrong, because, in their future, Momentum (the power source of the city) will end up causing the (near) extinction of humanity and, possibly, life on earth in general. Also, to be fair, it's not like destroying Neo Domino City was their first attempt at changing the future, as it's implied that they tried many other things before their current plan, so it's not that they didn't try other options, it's that the other options simply didn't work.
Akatsuki no Yona has Soo-won, who kills the protagonist Yona's father King Il and drives her out of the castle. However, he is shown mourning when he hears news that she died, covered for her when they accidentally meet from his subordinates, and is shown to love his country deeply, and improved and strengthened their country as king and is considered a "good king".