Tougou organized the "Outlaw" basketball team to oppose the school's all-girls basketball team.
The evil exchange students in the Kyoto arc resembled some of the students of class 2-C.
In Naruto, Gaara is the titular character's evil counterpart, as a boy who spent his childhood tormented by the demon inside him and abused by those around him. He represents what Naruto would have become if not for his True Companions.
Kabuto too, in an inversion. Realizing that Naruto is practically a good counterpart to himself, decides to take on Orochimaru's cells to mimic being a jinchuriki like Naruto. He also undergoes training under the White Snake Sage to become a Sage just like Naruto.
Nagato is also an evil counterpart to Naruto, especially since he's an Uzumaki. He plays Dark Messiah to Naruto's Christ figure.
Aaand now there's Obito as well, since he was explicitly compared to Naruto earlier in the story, before we knew he was a villain. And by villain, we mean the mask wearing Tobi who would've killed a minute old baby and sic a massive demonic fox on a woman weakened from pregnancy if he wasn't stopped. Ouch. And the parallels just keep on mounting with Obito becoming a Jinchuriki and being revealed that he is also an orphan who never met his parents.
Practically every antagonist has some quality that represents how one of the good guys could have gone horribly wrong.
Tsubasa in Kannazuki no Miko is Souma's evil counterpart as well as his older brother.
Vicious is Spike's Evil Counterpart in Cowboy Bebop. They share identical histories as crime syndicate assassins, and once worked together. Spike gave up his killing life after a near-death experience, but Vicious never did, and holds Spike in contempt for betraying his "true nature".
Similar to Vicious, Creed serves as Train Heartnet's Evil Counterpart in Black Cat, both were ruthless assassins in a morally ambiguous organization who had tragic histories. While Train becomes more humanized due to Saya's influence, Creed becomes more and more unhinged.
The anime Gate Keepers features a Dark Gate Keeper known as "Shadow", who it turns out became embittered with humanity by a family tragedy that he tried (and failed) to avert.
Tullece from the third Dragon Ball Z movie, The Tree Of Might. His entire character was based on the idea of what kind of person Goku would have grown up to become if he had never cracked his skull and gotten amnesia.
Yajirobe meanwhile was never a villain, but was a short, dim-witted and spiky-haired man who lived alone in the middle of nowhere, phenomonally strong and obsessed with food, mirroring Goku at the start of Dragon Ball. The contrast here was that Yajirobe was lazy, cowardly and generally much less pure compared to Goku's much more earnest demeanor. A kind of Chaotic Neutral Counterpart.
Both Piccolos were the evil counterpart of Kami. That is, before Piccolo makes his Face-Heel Turn and they remerge.
Yugi's opponent Pandora in Yu-Gi-Oh! used an alternate art version of Dark Magician that seemed to be an evil version of Yugi's own, having blood-red robes and a maddening expression, compared the the royal purple attire and gentle face of Yugi's version.
Yu-Gi-Oh! GX: Whenever someone turns evil, 9 times out of 10 they'll acquire an evil version of whatever cards they usually play:
The Evil Counterpart trope doesn't just apply to characters; the Archangel, the cool battleship of the main characters, gets an Evil Counterpart in the Dominion which is identical to Archangel in every way except for one: it's black instead of white.
Gundam Wing is none too subtle in setting up the Epyon to be Wing Zero's evil counterpart. Wing Zero's back mounted thrusters make it resemble an angel (made ridiculously blatant by the Wing Zero Custom), while the Epyon resembles a devil and a dragon while transformed. The 2 suits are similar in their construction: they both can transform into a jet mode, and they both contain a Zero System. However, they are also opposites: Wing Zero has a super-powerful gun, Epyon has a super-powerful sword. Also, the two Zero Systems are hinted to work in different ways, with Wing's "showing you the future", and Epyon's "showing you your death".
Interestingly though, the On the Next narration for Epyon's introduction episode says it's evil "just like Zero"; presumably this refers to the ZERO System rather than Wing Zero itself.
It was under the influence of ZERO that Quatre went Ax-Crazy. Wu Fei, on the other hand, just used it for a vision quest.
Code Geass has Schneizel vi Britannia, who sometimes seems like a good Counterpart when compared to his Magnificent Bastard of a little brother, Lelouch, a fact mirrored by their color preference in chess.
It's possibly a closer match with Charles, Lelouch's father. Once he takes the spotlight, we see that his past and personality are surprisingly similar to Lelouch's, except that Lelouch never reaches the point where he'd marry his buxom subordinate.
Speaking of buxom subordinates, it wouldn't be a stretch to say that Marianne is Kallen'sEvil Counterpart. Both are highly capable insanely hot Action Girl Knightmare Frame pilots that are completely devoted to their Non-Action Guy men. The crucial difference is that Marianne is a Lady Macbeth with no moral compass while Kallen's moral framework is so strong that she chooses her belief in what's right over the man she loves.
The Geass video game introduces twin princes Castor and Pollux, who are more directly Evil Counterparts; like Lelouch, they're amoral Chessmasters with Magical Eye powers, but unlike him, they have absolutely no problem using their Geass to make people their slaves.
Kuze is really similar to the Major, the series protagonist. They both were the 2 only survivors of a plane crash as children of about the same age who became friends in the hospital until they both got their first cybernetic bodies and lost contact. While the Major became a police officer working for the government, Kuze became a terrorist opposing the state. Both share the same goals of helping and protecting the people from corruption and crime, their only differences being which side of the law they chose to stand on.
The companion parallel: Touma saved Index and Accelerator saved Last Order, whom are eerily similar in almost every way aside from one strange reverse.
Heaven Cancellor notes that they're 2 sides of the same coin. Both want to protect their loved ones, Accelerator by killing or at least maiming anyone who threatens them, Touma by simply beating them up and then locking them up or befriending them.
Umidori Kuroyoru is an evil counterpart to both Saiai Kinuhata and Accelerator. She has the same power as Saiai, but uses it more aggressively and is a jerk compared to the more cheerful Saiai. Accelerator notes that Umidori's personality and fighting style is identical to his prior to his Heel-Face Turn.
Fiamma of the Right is another counterpart to Touma, who even compares their powers and draws attention to their similarities. Both use their Right Hands to shatter something that someone worked desperately to obtain, except Touma uses his to solve the problems around him and Fiamma his own personal problems — selflessness versus selfishness. In their final battle, Touma points out the biggest difference between them: Fiamma observed the world and was disgusted by what he saw, so he wanted to "save the world" by wiping out the human race. Touma observed the world and saw evil people to fight and good people to protect.
The author's notes explain that Aureolus Izzard is what Touma would have become if he had failed to save Index.
Touma gains yet another evil counterpart in Othinus. Their powers both involve misfortune. Touma doesn't need a reason to help people. Othinus doesn't need a reason to destroy.
This happens to Optimus Prime from Transformers quite a bit, most especially in the Japanese series. In Robots in Disguise, this takes the form of Scourge, who mirrors Optimus's appearance and strength. The fact that he's not outright identical to Optimus keeps him from being an Evil Twin.
However, Nemesis Prime from Transformers Armada IS an Evil Twin, with his coloration being the only difference, as is the one that crops up in the backstory for Alternators/Binaltech.
Motormaster from the Generation 1 cartoon could be considered the original Evil Counterpart for Optimus Prime. He had the same alternate mode and was built to be just below Megatron in power.
Haruhi Suzumiya In the later novels, the whole SOS-Brigade is revealed to have an Evil Counterpart group—alien interface, esper, time traveler, and "god" (whose powers had for some reason transferred to Haruhi). They aren't really evil; they just have opposing goals. The only one not represented in this dysfunctional group is Kyon, who they try to win over in the latest novel.
Well, not all of them are evil. Kyouko seems to have bitten off more than she can chew, Kuyou is much more ambiguous but seems to run on Blue and Orange Morality, and Sasaki is actually not evil at all, and is secretly on Kyon's side, but Fujiwara goes completely insane and tries to kill Haruhi in order to remake the timeline in his own image. He also claims to be related to his counterpart, but we don't know if that's true or not.
Also, Ryoko Asakura for Yuki Nagato.
Aion in Chrono Crusade is clearly Chrono's evil counterpart; even their time manipulation skills are opposed or complementary in the anime. In the manga their powers don't seem to be quite as related, but instead it takes the For Want of a Nail path if you think about it — as revealed near the end of the manga, Aion became bent on his path for remaking the world and Pandaemonium when he received visions of Pandaemonium's memories on his coming-of-age day. If Chrono is his twin brother, that means that he probably was lined up to have the ceremony, as well. He never had a chance because of the hubbub Aion caused, but if Chrono had gone first instead of Aion, Chrono probably would've been the one to go crazy, and Aion would've been the "good" twin. The fact that Aion refuses to tell Chrono the truth and says it's "better this way" probably shows that he, himself, is aware of how close Chrono came to being like him.
Of course, irrespective of who's mad, Chrno has a retiring personality and tends to do what he's told, while Aion is the bossy type, so even if Chrno were evil, the fight would be very different...Good Aion would probably lead the same set of Nakama he does as a villain, and Evil Chrno would be utterly alone.
In the manga, Knives has a much better motivation for turning on humanity, and at the time Vash reacted with the same level of horror and rage, but his first impulse was toward suicide. Rem got in the way, got hurt, and the need to help her snapped Vash out of it, and shaped pretty much the rest of his life. This meant that Knives woke up without her there to steady him—but maybe that wouldn't have helped, since rather than freak out, he pretended to have suffered Easy Amnesia until he had the chance to stage a slaughter.
In the anime, Knives is an outright child sociopath whose hatred is as much about disdain as fear, and Vash's thought patterns come nowhere near mirroring his. They still have a lot in common, though. Being twin brothers and the only members of their species and all. Also, for some reason this version of Knives can keep up at Gun Kata with a gunslinger who's been fighting for his life for a hundred years. It punches up the symbolism.
In Fullmetal Alchemist, Father is Hohenheim's Evil Counterpart. He's also even weirder than him. Toward the end, Father becomes more like an evil counterpart to Ed, as his bishonen "God" form looks like young Hohenheim except with Father's cruel eyes, and Father's arrogance and obsession with gaining knowledge at all costs is a dark reflection of Ed's tendency toward Pride.
Wrath is an Evil Counterpart of Ling. Both cover Charles Atlas Superpowers and impressive swordsmanship with a front of Obfuscating Stupidity, and Ling's actual Papa Wolf attitude toward his friends and subjects is mirrored in Wrath's pretensions to being a Father to His Men. In reality, he really couldn't give a damn about his subjects. Also, just as Wrath is a human-turned homunculus, Ling gets turned into the second Greed. However, while Wrath lost his human identity in his transformation, Ling manages to maintain his consciousness and serves as The Conscience to Greed, since he willingly gave in. Wrath started life as the 12th candidate for Fuhrer and Ling is the 12th son of the Emperor.
King Bradley is also the Evil Counterpart to Roy Mustang. The first names are the biggest clue. They've got kind of a triad of kingship going, there.
Kimblee comes across as something of an evil counterpart to Scar. Both have destruction-based powers (which are used to violently destroy people whom they touch, and rely on tattoos) and invoke Light Is Not Good (although Scar is at worst an Anti-Villain). Also, Kimblee "created" Scar, delivering the injury that gave him his nickname and killing his whole family, and more generally the role of Kimblee and other State Alchemists in carrying out genocide against Scar and his people is the motivation for Scar's revenge.
To support this argument, look at the scene where Scar is standing on the roof with Kimblee on the ground, with Scar himself pointing how their situations were reversed from in Ishval. Also, Scar moved on past his focus on revenge while Kimblee's obsession towards completing his job never waned.
Scar has another evil counterpart in Bradley, who describes both of them as nameless warriors, and again, you have the perpetrator of genocide versus the victim of genocide.
In Chiko: Heiress Of The Phantom Thief, the titular Chiko has something of an evil counterpart in Angie, who started off as a sweet happy-go-lucky girl befriended Chiko. She just happened to be the daughter of the head of security of the museum Chiko and her fellow thieves were casing. Chiko willingly betrays her and conducts the theft, leaving her behind. One Wham Episode later, she's stuck on the top of a moving train with an Ax-Crazy Angie trying to drive an axe into her skull. Smooth, Chiko, smooth.
Like Vampire Hunter D, Rei-Ginsei is a weirdly beautiful Hunter with supernatural powers. Unlike D, he's egotistical, completely amoral, only helps beautiful women and doesn't hesitate to try to torture a child to death to get what he wants.
Tengen Toppa Gurren Lagann has Lordgenome, the Spiral King, a Spiral Knight who might be considered what Simon would have become if he hadn't had Nia to find the Anti-Spiral homeworld and therefore end the war in his favor.
Lordgenome: "There once was a man who fought like you, not realizing his actions would bring about the destruction of humanity."
Guame the Steady is Boota's Evil Counterpart. Guame is shown as a small critter accompanying a young Lordgenome exactly the way Boota does Simon.
Sensui from YuYu Hakusho is the protagonist's Evil Counterpart. Sensui was the spirit detective for Earth before Yusuke was and both had a strong binary belief of good/evil and human/demon. The main difference is that after Sensui accidentally witnesses the "Feast of Human Vices" those beliefs were shattered. Another 'more fragile and idealistic equals turning to the Dark Side.'
A better and lampshaped example would be Younger Toguro, who Yusuke would be if he gave into his Blood Knight tendencies, and stopped caring for his True Companions.
Setsuna has one in Tsukuyomi, the mad Shinmeiryuu swordswoman to match Setsuna in every major battle. Unlike Setsuna, Tsukuyomi is bloodthirsty, direct and wins by any means necessary. Setsuna is quiet, humble and rarely fights for anything other than her charge, Konoka. Plus they're both lesbians, but Setsuna's innocent and taciturn while Tsukuyomi likes to speak in Double Entendre and Subtext and is willing to do anything at all, at anytime she can (ironically, to Setsuna herself).
Kotaro seemed to be an one to Negi during the Kyoto arc, although he has since done a Heel-Face Turn and become The Rival.
In the Magic World arc, Big Bad Fate Averruncus appears to be one to Negi, as each is a cute boy with a group of female partners backing them up.
Fate's entire team is made up of Evil Counterparts, some obvious and some not. Anya's mirror is an Emotionless Girl who looks quite similar to Anya and likes the same element. Yue and Nodoka's opposites are the panty-less Emotionless Girl and the panther girl, respectively, although the only similarity between Nodoka and panther seems to be hair color and they hang out with their version of Yue. Haruna is vaguely connected to the girl with the lute, in that they are both artists (music vs drawing). Finally, as stated above, Fate is Negi's opposite. They both have female followers.
Aizen and Urahara are both extremely intelligent scientists whose conflict with each other consists of one protracted chess game. The difference between them is that Urahara cares about the people he has to use whereas Aizen refuses to trust or bond with anyone. Aizen was willing to break the universe to fix it whereas Urahara didn't think that was the right thing to do.
Aizen and Hitsugaya were both extremely powerful prodigies driven to loneliness and isolation because of that power. Aizen turned against the world because of that isolation whereas Hitsugaya worked through that isolation to find people he could bond with.
Grimmjow, a hollow with shinigami powers is the foil of Ichigo, a shinigami with hollow powers. They are both determined to become the strongest fighter and both have Blood Knight instincts. However, Ichigo controls his love of battle, believing he should fight only to protect, whereas Grimmjow believes battle lust should be indulged for its own sake.
Yumichika and Charlotte are both vain, narcissistic Blood Knights until Mood Whiplash reveals the truth. Charlotte shares the 11th division belief that "beauty" derives from physical prowess whereas Yumichika reveals that "beauty" derives from Undying Loyalty. He's secretly a Magic Knight sacrificing himself for the sake of his division's anti-Functional Magic code.
Szayelaporro is Mayuri's evil counterpart. Mayuri is an evil Mad Scientist who is motived For Science! The reason Szayel is far worse than Mayuri is because he believes science exists solely for him to achieve perfection whereas Mayuri genuinely wants to advance society's knowledge.
Nnoitra and Kenpachi are both sociopathic Blood Knights who are seeking a Worthy Opponent. However, Nnoitra is a hateful, misogynistic Deathseeker whereas Kenpachi doesn't hold grudges, respects his opponents and forms close bonds with those around him.
Starrk lampshades he and Kyouraku are counterparts but is proven wrong. Starrk simply wants companionship and friendship, so is honest in battle because he doesn't want to fight. Kyouraku believes fighting means there's been a failure to find alternative solutions, so it's best to end the fight quickly by any means possible.
Ichigo and the Lost Agent Arc Villain have similar powers and origins, but the villain can't handle being mistrusted by Soul Society, goes off the rails and begins a process of revenge that harms innocents as well as warriors. Ichigo understood the necessity for Soul Society's monitoring of substitute shinigami and accepted it as part of the responsibility of wearing the uniform. He also keeps a fight personal rather than dragging in innocents and using them as weapons.
Buggy the Clown from One Piece seemed to be introduced as an Evil Counterpart to Luffy; Indeed, their devil fruits are practically opposite in several ways, but similar in others (allow for long range attacking, provide invulnerability to certain kinds of attacks). While Luffy is irrepressibly cheerful, Buggy is constantly aggravated, etc.
It looks like Blackbeard is shaping up to be Luffy's Evil Counterpart in addition to the Big Bad. He's initially introduced as someone who has similar dreams to Luffy and similar ambitions, as well as the same Big Eater nature (though with completely different tastes in food). Then it turns out he takes things a bit further and will actually betray his True Companions and kill them to fulfill his ambitions. He even subtly points this out when he and Luffy reunite in Impel Down and hints that they're Not So Different. It helps that his crew mimics Luffy's as well, with Van Augur as counterpart to Usopp, Shiliew to Zoro, etc.
The Blackbeard pirates except perhaps the original members don't think of each other as nakama and some members has expressed an interest in dethroning Blackbeard as leader. Some of them stated that if Blackbeard wasn't able to steal Whitebeard's powers, they would have just abandoned him to the Marines. Also, many of the members are Gonk in contrast with the Straw Hats who are good-looking, cool or cute.
Another similarity is that, despite being a Jerkass and coward, he and the rest of the Blackbeard Pirates (Besides maybe the new members from Impel Down) all believe in destiny and dreams (Which seems to be a trait of the people who have the D initial)
Frankly you could say that most every Big Bad Luffy's encountered along the way was something of an Evil Counterpart with Crocodile being an embittered ruthless Chessmaster that gave up on dreams and Moria revealing that he lost his beloved True Companions in the New World. They seem to act as chilling reminders of what Luffy may become if he doesn't hold onto his dreams and his friends.
Interestingly, Admiral Akainu could serve as one for Ace. Along with the heatpowers, they're both devoted to their own sense of justice; Akainu adheres to absolute justice, hunting down any criminal, while Ace was determined to take down Blackbeard for his murder of a crewmate. These codes even go beyond those of their superiors/captain, as Sengoku and Whitebeard both have their limits. What separates them is that Ace genuinely cares for others, while Akainu doesn't even hesitate to murder his underlings if they oppose him.
Which makes it really harsh when the Evil Counterpart wins, and Akainu kills Ace.
Lately, Hyouzou, the New Fishman Pirates' assassin, is this to Zoro. Both of them are powerful swordsmen, enjoy drinking and have a calm demeanor. However, Zoro has never been shown drunk while Hyouzou seems to become drunk very easily, putting him in a state where he blindly attacks anyone and everyone around him. Hyouzou only works with people who offer him the most money, while Zoro is only willing to fight for money at all when it's absolutely necessary, preferring instead to fight for his ambitions and his True Companions.
GaoGaiGar: Each of the 11 Planetary Masters of Sol is an Evil Counterpart for a member of the main GGG crew, even though it's not immediately apparent which is which.
Back when Kinnikuman was a superhero, Kinkotsuman was introduced as his villainous counterpart; He was just as bad at what he did as Kinnikuman was. Unlike Kinnikuman, he was unable to eventually find a more fitting profession and slowly became less prominent as more serious villains started showing up.
In Full Metal Panic!, there's the Creepy Twins Yu Fan and Yu Lan, who are shown to have been through extremely similar wars and circumstances as Sousuke. Just like Sousuke, they're rather emotionless, extremely loyal to the person that took care of them, and their occupations are very alike. Main difference? Sousuke was adopted by Kalinin and the twins were adopted by Gauron. Funnily enough, Gauron (as elaborated on in the novels) is revealed to have actually tried to take Sousuke when Sousuke was young, but Sousuke refused. 5 years later, and Gauron is still fantasizing and obsessing over "beautiful" Sousuke. If there's anything Sousuke did right when he was young, it was knowing who to accept as his father figure.
Gauron himself is quite similar to Sousuke. They're both Almighty Janitor soldiers with little allegiance to anyone except their own desires(at first). While Sousuke develops genuine bonds with other, Gauron is driven by his depraved interest in Sousuke.
In Katekyo Hitman Reborn!, the members of the Varia are meant to be tailored as Evil Counterparts to the Vongola Family. Xanxus is Tsuna's counterpart, as both have similar Dying Will Flames and both are competing for the same position as the boss. The only one that is somewhat unclear is the Evil Counterpart to Mukuro—Mammon. Especially since Mammon is mainly motivated by money and isn't nearly as cynical or scary.
Every major robot villain in Astro Boy is an evil, or at least morally ambiguous counterpart to some extent. What makes them interesting is how each one completely inverts a major aspect of Astro's personality or show what he'd be like if things had happened differently, or to underscore the fact that who he is rather than what he is makes him a hero, for example:
Atlas, who has become Astro's biggest rival over the years. Though he was little more than a violent thug in his first appearance, he was later updated in the 80s anime as a Composite Character of Atlas, Astro's "brother" Cobalt & the Blue Knight. In the 2003 series, with the Blue Knight retained as a separate character, though, their conflict was more personal than political. Both had terrible relationships with the men they called "father", but had very different ways of dealing with it; Atlas' involving kidnapping, industrial sabotage & attempted murder. What makes it more poignant is the fact that they were both based on the same technology, adding a layer of "there but for the grace of god go I" for Astro, that an advanced AI can choose between good & evil.
Astro II, a "more human" version of Astro, including human vices such as lust & sloth.
Nearly every season of Sailor Moon has a set of villain counterparts to the Inner Senshi. R has the Akayashi Sisters (Koan-Mars, Bertier-Mercury, Petz-Jupiter, Calaveras-Venus), S has the Witches 5 (Eudial-Mars, Mimete-Venus, Tellu-Jupiter, Villuy-Mercury), SuperS has the Amazoness Quartet (Cere Cere-Venus, Palla Palla-Mercury, Jun Jun-Jupiter, Ves Ves-Mars).
This carried over to at least one video game adaptation, Sailor Moon: Another Story. In that game, while it brought back all their old foes to that point as bosses, the main villains (other than the Big Bad) were the Oppositio Senshi, 5 teenage girls with powers mirroring the Inner Sehshi, and names based on Babylonian gods and goddesses: Sin (God of the Moon), Nabu (God of Wisdom), Nergal (God of War), Marduk (God of Thunder and leader of the gods), and Ishtar (Goddess of Love).
In the manga, Queen Nehellenia of the Dead Moon Circus was seen as a shadowy, mirror reflection of Queen Serenity. Likewise, Nehellenia's kingdom of the Dead Moon was hidden inside the shadow of the moon's center.
In InuYasha, this is the Big Bad's motivation. Naraku seems to hate InuYasha specifically due to their similarities: they have the same half-demon nature, causing loneliness to both, but InuYasha forms bonds to soothe his loneliness, while Naraku destroys the bonds of other people to make himself feel better. Naraku's frustration over this is the reason why he never really does anything but try to power himself up or ruin InuYasha's life (symbolically destroying his own half-breed nature). InuYasha also points to this as the reason Naraku particularly disgusts him before their Final Battle.
Kikyo has an evil counterpart in the black priestess Chubaki.
Jagi from Fist of the North Star was initially built up as an evil counterpart to Kenshiro, having the same 7 scars and everything. Whereas Kenshiro uses his skills to protect the weak and punish villains, Jagi uses Hokuto Shinken to terrorize villagers. Subverted as it is revealed that Jagi never truly mastered Hokuto Shinken and that he's not the only other student to learn Hokuto Shinken from Master Ryuken.
Hei in Darker Than Black has a couple of characters who qualify as evil counterparts: There is Wei, a fellow Chinese Badass whose psychopathy contrasts with Hei's relative restraint. Like Hei, Wei is also one of the few contractors shown to be capable of emotion, but his are all negative to Hei's positive ones. Another character Nick has the same power as Hei, the same nice guy persona, and has the same goal of finding his dead little sister, but he wants to achieve it through murdering people; Harvest, the Big Bad of the interquel manga has the opposite power to Hei- while Hei's power involves creating material on an atomic level, Harvest's involves destroying it; Mina in season 2 wears a similar costume/shares similar weaponry to Hei and is also The Stoic, but is also a dark reflection of Kirihara, sharing a similar background of being The Ojou.
In Girls Bravo, the main character Yukinari and the Big Bad Yukina, as if the similar names weren't a big enough clue. While in some ways they are complete opposites — he's a powerless Non-Action Guy who is allergic to women but generally doesn't hold a grudge against them ,and she's an Extraordinarily Empowered Girl who is allergic to men and wants to kill all of them — both of them have dealt with a great deal of pain in their lives that led to them both being Allergic to Love with the opposite gender. In the end Yukinari is able to stop her from committing gendercide simply by gently talking her down and helping her deal with the insecurities that created the situation in the first place. Unfortunately for Yukinari, his former Evil Counterpart falls in love with him and becomes a YandereStalker with a Crush with a bad habit of sneaking into his bed (naked) while he's sleeping. Also, while she isn't allergic to him, he is still allergic to her.
Truly explored in Magical Girl Lyrical Nanoha A's Portable, where Nanoha, Fate and Hayate have Evil Twin counterparts for themselves. Stern the Destructor a.k.a. Material-S, Levi the Slasher a.k.a. Material-L, "Lord" Dearche a.k.a. Material-D. However, all of them turn out to be Anti Villains in the second game.
Subverted with Fate and Levi. While Fate and Arf suggest that Fate would become like Levi if she never met Nanoha and the others, Nanoha denies it because Fate would still have Arf and Fate is stronger than they think. In the second game, Levi becomes even less similar to Fate, as she has become a Genki Girl, a Dumb Muscle and a Blood Knight. Levi is the more or an Evil Counterpart to Alicia if she ever got Fate's magic skills.
Also subverted with Nanoha and Stern. Despite they have similar powers, Stern has almost nothing in common with Nanoha, except their apparent love for fighting.
Hayate and Dearche are the closest example if you compare the the three Aces with the Materials. Both of them have their own guardians (Hayate's Wolkenritter, and Dearche's two retainers), both are the Supreme ChefTeam Mom for them, both have the highest magic power of the respective trio, they are the superior of the three, but they are also the Squishy Wizard. Both have also hacked into the system program of two extremely powerful People Of Mass Destruction (Reinforce and Yuri), respectively, making them controllable. Nanoha thinks Dearche even invokes this when she calls U-D "Yuri" (that is her real name in the first place), assuming that she renames U-D like Hayate renamed the Book of Darkness to Reinforce. Dearche is basically Hayate if the latter is Drunk with Power and gets an Awesome Ego.
Surprisingly, in ability wise, Curren can be considered to the Vivio's. Both have the ability change their body age, as much as they want. But unlike Vivio, she's lacking in maturity and complete asshole, while Vivio is Wise Beyond Their Years and nice to everyone else.
Reitei Lyon (an ice mage trained by the same master) is this to Gray, in addition to Rival Turned Evil.
Gajeel, the Iron Dragon Slayer, is introduced as this to Natsu, the Fire Dragon Slayer, but after a Heel-Face Turn he becomes Natsu's rival.
In the Tenrou Island arc, Zancrow of Grimoire Heart is Natsu's, being a psychotic fire mage who can also eat flames like Natsu.
Angel of the Oración Seis seems to be a pretty blatant one of the protagonist Lucy; they're both Celestial Spirit Mages that possess Golden keys. While Angel is overwhelmingly powerful, Lucy is still relatively naive and relies more on skill. The biggest difference seems to be in the treatment of their spirits. Lucy treasures all of them and treats them well, while Angel is willing to deliberately injure them to achieve victory.
Master Jose of Phantom Lord was one for Makarov, before it became painfully apparent that Jose couldn't stand up to him in a fight. Most of his magic was darkness based, while Makarov's spells (other than his size increase) are light based. The next one is Master Hades of Grimoire Heart. In addition to being the previous guild master of Fairy Tail and Makarov's former mentor, he's the only one in the entire series to have beaten Makarov in a fair fight.
Sabertooth gives us a lot of ones. Sting and Rogue, the Twin Dragon Slayers, for Natsu and Gajeel, respectably. Orga, who is the Lightning God Slayer, for Laxus. And Rufus whose Memory Make magic is creation based and is a counterpart for Gray. An unusual one is the Sabertooth guild master, Jiemma, who seems to be what Laxus would have turned into had he not been stopped from his takeover attempt by Natsu and Gajeel.
Whereas Kenshin wants a peaceful Japan in which war will no longer be necessary, Shishio, the man who replaced him as hitokiri is The Social Darwinist and wants to create a Japan that is a proud warrior race. Also, while Kenshin has neat X Marks the Hero scars, Shishio was badly burned and wraps himself in bandages.
Shishio's follower Soujirou Seta is also one to Kenshin. Kenshin endured a sad childhood and was orphaned before being adopted by a master who trained him in swordsmanship. In personality, Kenshin didn't start out all that happy but eventually took on a cheerful Obfuscating Stupidity. As a dark mirror to Kenshin, Soujirou grew up in an abusive family and found an Evil Mentor in Shishio, who gave him the encouragement to become a Self-Made Orphan. In terms of personality, Soujirou has a more extreme version of Kenshin's forced cheerfuless, being a Stepford Smiler who is incapable of showing (and to an extent feeling) any emotion.
To complement this, Shishio serves as one for Kenshin's master Hiko Seijuro. Both are powerful and influential mentors who inspire ideologies in their pupils. While they're both hardened in some way, Hiko holds some optimism towards Kenshin's path. Shishio, while he does care about him, brainwashes Sojiro into his ideology. Hiko comically abuses Kenshin but respects his pupil's decisions.
Sanosuke has evil counterparts in Cho, one of Shishio's men, and later, Banjin, a follower of Enishi. Both of these characters have dress and hair styles clearly similar to Sanosuke's, and while Sanosuke is a Boisterous Bruiser with a code, Cho and Banjin take a love of fighting to Blood Knight levels and have no real morals.
Monk Anji is also one of Sanosuke. They're both fist-fighters who suffered a the loss of loved ones; Sanosuke with Captain Sagara and Anji with all of his adoptive children. To deal with this pain, they turned to violence. When they meet Kenshin and Shishio respectively, the dynamic is also reflected. Sanosuke, while vitriolic to Kenshin, trusts him completely. Anji is merely siding with Shishio for his own reasons.
Earlier then that, there's Shikijou. Like Sano, he enjoys fighting and has immense loyalty to the one who defeated him (Aoshi), but the depths to which he's willing to go for strength disgusts Sano (this is played up more in the manga).
Usui is one for Saitou. They're both stabbing specialists, and compared to the leaders of their factions (Shishio and Kenshin) are relatively indifferent. Saitou merely wants to take out Shishio because "he happens to be on the opposite side". Usui cares only about boosting his ego. Saitou's rivalry with Kenshin is a mirror of Usui's relationship with Shishio. However, Kenshin and Saito are mutual rivals, while Usui is chasing after Shishio. While both are consumed by their rivalry, only Usui allows it to define himself and mask his own insecurities. Usui shows what Saitou could've become if he lost his code and only focused on the past.
Enishi Yukishiro, mentioned two points above, is an Evil Counterpart to Kenshin on an even more personal level than Shishio. Both he and Kenshin received lasting physical marks from the same incident (the accidental death of Tomoe, Kenshin's wife and Enishi's sister, at Kenshin's hand)—Kenshin got the second part of his famous cross-scar, while Enishi got Locked into Strangeness via his hair turning white from the shock. However, while that same incident motivated Kenshin's future Thou Shalt Not Kill and The Atoner mentality, Enishi turned Ax-Crazy and bent on revenge. To further the counterpart theme further, their animal motifs are traditional opposites (Kenshin's fighting style is reminiscent of the dragon, while Enishi's is akin to the tiger) and Enishi's Watou-jutsu sword techniques are coincidentally perfectly able to counter Kenshin's Hiten Mitsurugi techniques.
From early in the series we have Udo Jine, who was a hitokiri during the Bakumatsu like Kenshin. Unlike Kenshin though, Jine is an Ax-CrazyBlood Knight that could not give up his life as a killer after the Bakumatsu due to his bloodlust.
In Eyeshield 21 Clifford D. Louis of The Pentagram is a pretty obvious Evil Counterpart to Hiruma of the Deimon Devil-Bats. They're both talented poker players and Evil Genius quarterbacks, who invoke Blond Guys Are Evil and love a good challenge. They even both wear #1 jerseys. The only real differences are Hiruma's preference for trick plays, and Clifford's greater speed. Before Clifford arrived, Marco of the Hakushuu Dinosaurs was a slightly less obvious one: he's a Manipulative Bastard to Hiruma's Trickster Archetype, and unlike Hiruma, prefers to avoid facing strong teams. At the same time, though, they both favour using any tactics necessary to win, use intelligent plays to compensate for a lack of natural talent, Determinator their way through crippling injuries, and get the very best out of their team. You could arguably throw in the Ojou White Knights' Takami as a Good Counterpart to the both of them, as he shares almost all of those same qualities, but without the penchant for brutality.
Suitengu's motives in Speed Grapher reveal him to be an Anti-Villain counterpart to Saiga. They have more shared history than they know.
Medaka Box: Besides obvious parallels between the protagonist, Kumagawa is also a dark mirror of Zenkichi, sharing similar traits while sitll appearing to be complete opposites. While Zenkichi is a tsundere, Kumagawa is a compulsive liar. Similarly, they're both attached to some of the most powerful figures in the story; Zenkichi to Medaka, Kumagawa to Ajimu. While Zenkichi doesn't think much his abilities, Kumagawa claims to be epitome of weakness, yet both are some of the most determined people in the series.
Puella Magi Oriko Magica: Oriko and Kirika are either Evil or Extreme Counterpart to Madoka and Homura, respectively. Both Madoka and Oriko have angelic magical appearance, both aim to save the world. Homura can stop time, Kirika can slow down time. Homura will do anything to save Madoka, Kirika will do anything including mass murder for Oriko's vision. Homura's and Kirika's obsession has to do with Madoka and Oriko respectively being nice to them.
The tragedy of the Count in Gankutsuou centers around Fernand's betrayal of Edmond out of love for Mercedes. Skip forward one generation, and Albert has many of the traits Edmond did (most obviously an amazing ability to attract friends and followers), with Franz as his Fernand and Eugenie as his Mercedes. The difference is that Franz is too loyal to Albert to do anything to harm him and it is due to this that Albert retains his kind heart and life even after all the crap the Count puts Albert through and becomes an All-Loving Hero who saves Edmond Dantes' soul at the end.
In Pokémon, Paul is this to Ash more than any other Rival character. Ash is kind, helps others, respects his opponents, sees the true potential in all Pokemon, and travels with True Companions, also treating his Pokemon as such. Paul is mean, out for himself, mocks those he beats as "weak" (including Maylene), tosses away Pokemon who don't immediately measure up, travels alone, and puts his Pokemon through Training from Hell.
Gary and Trip were more provincial dicks, but were never shown to mistreat their Pokemon and grew out of their behavior once character development set in.
One of the earliest examples is an Evil Counterpart for Kenichi—Odin, the First Fist of Ragnarok otherwise known as Ryuto Asamiya. They were inspired by the same childhood incident (seeing a then-5-year-old Miu beating up adult thugs all by herself), but while Kenichi was motivated to fight for justice (something he wouldn't remember until years later in the present day), Odin was motivated to gain power. Shortly after the aforementioned incident, the two had a fight for a yin-yang pin Miu had given Kenichi in exchange for a cat pin she wanted; Kenichi won the fight, but then offered the pin to Ryuto anyway and suggested to pretend that Ryuto had won—which only wound up offending Ryuto's pride and sparked his Start of Darkness.
Natsu Tanimoto, a.k.a. Hermit the Sixth Fist of Ragnarok, had a brief Evil Counterpart in Berserker, the Second Fist, after Tanimoto defected from Ragnarok; while Tanimoto advocated hard work and training, Berserker was a naturally-gifted fighter with no formal training who could nevertheless give Tanimoto a sound thrashing during their clash. (It's played with, however, in that Tanimoto is currently going through the Heel-Face Revolving Door.)
Kisara Nanjo was originally touted as an Evil Counterpart to Miu back when she was Ragnarok's Eighth Fist, Valkyrie. Following her Heel-Face Turn, she got her own Evil Counterpart in Freya, the Third Fist, because she used to be one of Freya's underlings and also concerning their differing views on the use of weapons (Kisara, while not begrudging Freya for using weapons, simply didn't feel she herself should resort to weapons in order to stand alongside men as a fighter); eventually though, Freya had her own Heel-Face Turn and the two remain friends (maybe).
Since Yami is the organizational Evil Counterpart to Ryozanpaku, by default the members of YOMI (all disciples of the One Shadow Nine Fist members of Yami) become Evil Counterparts to Kenichi. One of the more notable counterparts in this regard would be Sho Kanou; both he and Kenichi were motivated by affection for Miu and Kanou even pulled a Redemption Equals Death because of her. As well, Kajima Satomi (the disciple of the One Shadow) may eventually turn out to be this for Kenichi as well.
The earliest master-class example would be Kensei Ma'solder brotherSougetsu Ma—both men are well-known fighters from China, but Sougetsu is considered a disgrace on the family name due to his embracing of the killing-fist philosophy and his turning to crime. And now Sougetsu is a member of the Nine Fists, making him an even greater counterpart to Kensei.
Two members of the One Shadow Nine Fists group are Evil Counterparts for two members of Ryozanpaku—"God Fist" Akira Hongo for Sakaki Shio and Agaard Jum Sai for Apachai Hopachai. In both cases they're childhood friends of their respective good counterparts and fighting partners who turned to the dark side. However, in Agaard's case, he turned to the killing-fist philosophy out of pure instinct, a fact Apachai understands and respects; while Sakaki's and Hongo's differing philosophies came out of the same incident that tore apart their comradeship—the death of their mutual friend at Hongo's hand during a fight to apply for a position with Yami, which prompted Sakaki to utterly reject the killing-fist philosophy. Both Nine Fists members are an interesting case, however, in that Agaard is an Affably EvilFriendly Enemy and Hongo is a Jerk with a Heart of Gold who will Pet the Dog occasionally and has high moral footing.
Yet another master-class example: Alexander Gaidar, the One Shadow Nine Fists' resident Command Sambo master, is an Evil Counterpart to Ryozanpaku's judo master Akisame Koetsuji where appreciation of artwork is concerned. Both men are extremely talented sculptors, and are capable of making impressive pieces of artwork out of the steel and stone of their surroundings even while they're fighting each other.
Souji Mikage is one to Utena herself in Revolutionary Girl Utena: both are duelists despite not being on the Student Council, both duel with sabers, and both fight for the sake of a loved one: Mamiya in Souji's case, and Anthy in Utena's.
Busou Renkin's Kazuki has his Anti-Villain counterpart Victor. Papillon is also the same as Kazuki in that they are motivated by the concept of a "second life". But while Kazuki was brought back to life by Renkin, Chouno wants to become immortal by becoming Homunculus.
Hellsing: Alucard's counterparts in Iscariot and Millienium are father Alexander Andersson and the Captain.
In the Junji Ito story Intersection Pretty Boy the main character strives to be that to the titular Pretty Boy, a mysterious guy dressed in black spreading curses among girls asking him hints about their love life.
Upon failure it's mentioned he has evolved into another Pretty Boy, this time a good one, able to spread blessings and good wills, thus finally opposing his enemy at his own level.
In one episode of Kazemakase Tsukikage Ran, Ran and Meow are pitted against two female bandits, one a samurai like Ran and the other a martial artist like Meow. Meow is however less than pleased to find out that her counterpart is a dumpy middle-aged woman.