In the Harry Potter books, Big Bad Voldemort is Harry's counterpart, having been raised in similar conditions and circumstances, and accidentally given some of his power to him, but taking a different moral/ethical path.
Additionally, Gellert Grindelwald is the dark twin of Albus Dumbledore.
Bellatrix Lestrange is the Evil Counterpart of Sirius Black. They grew up in the same environment and have similar temperaments. They're both skilled magically, and they resemble each other physically. They're both very devoted to their respective sides, and would do anything to protect those they care about. Their deaths even parallel each other, which Harry points out.
Bellatrix is also an evil counterpart to Hermione Granger. Hermione is as devoted to Harry as Bellatrix is to Voldemort. Both intelligent and powerful witches, willing to go to extremes for their purposes.
Many fans look to Dolores Umbridge as an evil counterpart to Minerva McGonagall. Both are senior members of Hogwarts and known as strict disciplinarians, but McGonagall is stoic but ultimately good, while Umbridge is a very thorough Bitch in Sheep's Clothing. They butt heads often after Dumbledore departs. They also both have cat Patronuses.
Some interpret Peter Pettigrew as Ron's Evil Counterpart. They're both overshadowed by their more popular/gifted friends, but while Pettigrew only latches onto strong people, Ron truly cares about Harry and Hermione. Immediately regretting abandoning them in the last book counts.
Peter Pettigrew and Neville. They both start out as cowardly people who aren't particularly powerful, but Neville chooses to do the right thing and becomes braver and more powerful as the books go on, and stays loyal to his friends, while Peter chooses to do the easy thing and becomes loyal to the most powerful person around (who is Voldemort) and betrays his friends.
Remus Lupin and Fenrir Grayback. While they're both werewolves (and Remus was bitten by Grayback as a child), Fenrir goes after and attacks people, particularly children, while Remus tries his hardest to avoid hurting someone.
Molly Weasley (née Prewett) and Narcissa Malfoy (née Black). Molly is the warm, caring matriarch of one of the Wizarding World's most prominent anti-Voldemort families, and she's the mother of Harry's closest friend, acting as a surrogate mother for him. Narcissa is the cold, manipulative matriarch of one of the Wizarding World's most prominent Pureblood supremacist families, and she's the mother of Harry's bitterest enemy. While Molly believes in and fights for her side's cause, Narcissa defects first chance she gets. In both cases, this stems from loving their family.
R.A. Salvatore feels the need to state that Artemis Entreri is Drizzt's "dark mirror" every time the two meet.
This is partially because Artemis himself became obsessed with the concept of them as opposites, to the extent that Jarlaxle faked Drizzt's death and hoped that Artemis would drop it now.
Interestingly, Salvatore would later write a far better example of an evil counterpart for Drizzt in the form of King Obould Many-Arrows (not an original character for Salvatore, but he gave him all his real characterization). Like Drizzt, Obould is an exceptional member of an Always Chaotic Evil race that sees the obvious flaws in his native society and rejects them. Unlike Drizzt who chose to run away from drow society and strike out on his own, Obould grabs orc society by the neck and forces a fundamental change in it, waging a brutal war not for the sake of plunder as most orcs do, but to carve out a kingdom where orcs can form a true civilization. What makes this interesting is that Salvatore never points out the parallels between them.
In the Inheritance Cycle, Murtagh was already a slightly darker version of Eragon before Galbatorix recaptured him and forced him to become a Blood Knight.
Nasuada has to keep a close reign on her modus operandi, so that she doesn't turn into Galbatorix.
Granny Weatherwax's sister Lily, in the novel Witches Abroad. A somewhat ironic example, as Lily considers herself to be the good one, and Granny thinks of herself as an Anti-Villain, being a prime example of Good Is Not Nice. It's played with a bitnote What a shock. since the Theory of Narrative Causality means that any magically inclined siblings on the Disc will eventually form a Good/Evil pair, and the reason Granny is mad at her sister is because she didn't want to be the Good one and was forced into the role when Lily ran away.
Lord Hong to Lord Vetinari in the novel Interesting Times. Though the two never meet (and Vetinari may not even be aware of Hong's existence) the uncanny similarities of hyper competence, forward thinking, manipulation and the ability to wield power are made clear. Hong is a younger Vetinari with all the sense of duty channeled into personal ambition. Hong's mistake is that he thinks everyone is like the Agatean people; he doesn't know people and how to push their levers whilst Vetinari is a master of getting people to do what he wants them to do, even though they think they aren't.
In general, members of the Assassins' Guild seem to be the evil counterparts of Vimes — he is a gritty Technical Pacifist who fights dirty whereas they are unsurprisingly well-bred hired killers.
Vimes and Carcer in Night Watch, to the point where the book itself notes that Carcer is an inverted version of Vimes. Both are extremely determined and driven men with similar cynical outlooks on the world, believing that law and order are essentially illusions, but whereas Vimes makes it his life's work to uphold those illusions Carcer does his best to shatter them. Vimes is Commander of the Watch, Carcer specializes in murdering coppers. When cast back in time, both manage to become sergeants and leaders of their respective sides through sheer audacity alone. It's implied that Carcer is what Vimes would have become, had Keel not taken him under his wing as a boy.
Subverted with Damasen, who is the good counterpart to the war god Ares/Mars.
Also Alcyoneus' lair to Camp Jupiter.
Jason, Piper, and Leo each have an evil counterpart to themselves in "The Lost Hero".
Jason has Lityerses, a handsome and skilled swordsman who uses a golden sword and has scars on his body like Jason does, but he is arrogant and intentionally flaunts his attractiveness, unlike Jason. In even further opposition to Jason, who cares deeply for his sister Thalia, Lityerses cares very little for his sister, who was turned to gold by their father King Midas. Both Jason and Lityerses like Piper, as well.
Piper has Medea, another attractive individual who can charmspeak like Piper, but uses it for her own gain, unlike Piper. She also has connections to the Giants, like Piper does. Unlike Piper, Medea is confident in herself and her abilities. Both women have had a relationship with a hero named Jason, although Piper's was not real but Mist-induced (although it does eventually happen). To make it even worse, Medea manipulated Piper's father Tristan Mc Lean's assistant Jane into tricking Tristan and allowing him to be kidnapped by Enceladus, who tried using him to blackmail Piper into betraying Jason and Leo.
Leo has two. The first is the Cyclops Ma Gasket, who is immune to fire and a skilled mechanic like Leo is, but uses her skills against the Olympians. In opposition to Leo, Ma Gasket is the eldest member of her family who didn't leave her sons Sump and Torque to fend for themselves as Cyclopes should, while Leo is one of the younger members of his family who was thrown out into the streets by his family after his mother's death. The second is Khione, the goddess of snow. While Leo can control fire, Khione controls ice. They both have similar parentage as they are both a child of a god: Leo is the son of Hephaestus, while Khione is the daughter of Boreas.
Shiwan Khan, one of The Shadow's antagonists, had the same ability to "Cloud Men's Minds", and was one of the few villains to appear in more than one novel. In the 1994 film, the Evil Counterpart aspect of the characters was made much more explicit: both were trained by a mystic known as The Tulpu, but whereas Lamont Cranston turned away from evil, Shiwan Khan did not.
Ishamael for Rand. Both are the leaders of their respective side and are extremely strong in the one power. But while Rand believes in doing his duty and saving world, Ishamael became a Nihilist who wants to destroy the pattern because he believes that everything is meaningless, that the dark will inevitably win and that it his purpose to fight for the dark one. He also seems to view his role in the ever repeating pattern to convince the Dragon to submit to this view; during the darkest depths of his psychotic breakdown Rand considers whether his counterpart was in fact right and almost destroys the pattern himself after a bit of Nietzsche Wannabe speechifying of his own
In the last book, Demandred gets in on the action, with his persona as Bao the Wyld deliberately crafted as a counterpoint to Rand's as the Dragon Reborn. However, he's still not as good an Evil Counterpart to Rand as Ishamael is, which is fitting since the overarching theme of Demandred's life is that he's always second-best. As the commanding general of the Shadow, however, he may just be Mat's Evil Counterpart, since Mat becomes his opposite number on the side of Light during the Last Battle.
Lanfear for Moiraine: Both women assisted Rand and would have killed him if necessary. But while Moiraine just wants him to save the world and oppose the dark one, Lanfear is a Yandere darlfriend who wants him to serve the dark one.
Slayer for Perrin: Both have connections with wolves and dream powers. Both of them enjoy killing and they both tried to lead the two rivers villagers against trollocs
Taim for Loghain: Both are false dragons who serve Rand reluctantly and both want glory. But unlike Logain, Taim is a darkfriend who wants to help the dark one triumph
Elaida for Siuan: Both are Amyrlins who were extremely powerful channlers, plot and manipulate others, want to control the dragon reborn and are motivated by foretellings about the dragon reborn. However Elaid is far more arrogant and organizes a coup, wants to kidnap and control rand to satisfy her ego and while Siuan tries to train Egwene into being her successor, Elaida wants to make Egwene her servant.
Recent Star Wars novels have taken the unfortunate fact that Shira Brie/Lumiya and Mara Jade are the same recycled character concept and chosen to emphasize the fact that Lumiya is Mara Jade's Evil Counterpart. The Legacy of the Force series, for instance, has for the first time confirmed that Shira Brie was part of the same Emperor's Hand program as Mara Jade and equal to her in rank, and, ironically, that if she had been nearby when the 2nd Death Star blew up and been given the task of horribly murdering Luke Skywalker, she could very likely have been the one redeemed by love who ended up marrying Luke instead of being horribly disfigured and eventually killed by him.
When August Derleth took HP Lovecraft's ideas and ran with them, he posited a group of "good" counterparts of the Great Old Ones called the "Elder Gods." Brian Lumley took this concept even further in his Cthulhu Mythos novels, with appearances by the Elder Gods Kthanid (a good Cthulhu) and Yad-Thaddag (a good Yog-Sothoth).
John Sunlight, the only villain to face Doc Savage more than once in the novels, had many qualities in common with Doc.
An even more obvious Evil Counterpart appears in the Doc Savage Annual published by DC Comics. It featured Siegfried, a young man raised by one of Doc's former teachers under the training regime developed by Doc's father. Siegfried and his mentor were in service of the Nazis.
Un from Shinigami no Ballad, who is counterpart to the main character. Weirdly enough, even though she wields power of destruction, she is consider to be the being of creation, and that even though Momo's appearance are all white, she's actually Un's shadow.
Taken to its logical extreme in Neil Gaiman's Alternate Universe short story A Study in Emerald, where the reader gradually realizes that in this world the nameless detective who lives at Baker Street and helps the police with cases is Moriarty, and the culprits for the latest case he is investigating are Holmes and Watson. Although the nature of this society is such that Holmes and Watson are still the good guys.
Taken to another logical extreme in Kim Newman's "A Shambles in Belgravia" — later expanded into the book The Hound of the D'Urbervilles — which not only has Moran documenting Moriarty's "cases" as Evil Dr Watson, but also supplies him with an Evil Mrs Hudson (the madam Mrs Halifax), and Evil Baker Street Irregulars (the Conduit Street Comanche — a "tribe of junior beggars, whores, pickpockets and garotters"). And in his spare time, Moriarty breeds wasps, apparently out of sheer malevolence and balancing Holmes's retirement as a beekeeper.
In the Raffles series, Raffles and Bunny are essentially evil (or at least anti-heroic) counterparts of Holmes and Watson.
In Lois McMaster Bujold's Vorkosigan Series, specifically beginning in Brothers in Arms where the hero Miles Vorkosigan meets his evil clone in a battle of wits and subterfuge. An earlier novel, The Vor Game has the female mercenary Cavilo, who is as short as Miles is (but more obviously physically attractive) and has a very similar talent for disguise and subterfuge. On the other hand, while Miles is ultimately a very good and loyal person, Cavilo is a psychopath.
In The Book of the Dun Cow, the evil Cockatrice almost perfectly resembles The Hero, Chauntecleer the rooster, the only difference being Cockatrice's scaly gray body, tail, and red eyes. This causes Chauntecleer to be mistaken for Cockatrice at least once by his Love Interest Pertelote, although she is later reassured that the two are not the same.
In the Skulduggery Pleasant series; Caelan has shades of being this to Fletcher. Both are infatuated with Valkyrie, both are vain and good-looking, they're pretty ineffectual despite having access to incredible power, and are very much the outsiders in the group of protagonists, and would both happily live their own lives away from the danger and chaos of saving the world if Valkyrie weren't involved. The main difference between them is that Fletcher is a Technical Pacifist who hates violence, and Caelan, on the other hand has killed dozens of helpless mortal women over imagined slights.
A good indicator of this is that, although he's seriously hurt when Valkyrie breaks up with him, Fletcher is able to move past it and get on with his own life, whereas Caelan simply cannot let her go and decides to kill her for "infidelity".
This is because, after Character Development takes away Fletcher's cowardice and most of his arrogance, he's pretty well adjusted and normal, whereas Caelan, on the other hand is so batshit insane, he killed his mentor for trying to warn him off his obsession.
The Star Trek: Typhon Pact series presents the Breen Confederacy as an antagonistic counterpart to the United Federation of Planets. Like the Federation, the Breen draw on multiple races and cultures to form their membership, and no race is legally subordinate to another. However, where the Federation celebrates its diversity and the potential for new perspectives, the Breen fear bias to an extreme degree, and insist on hiding their diversity even as they utilize it. Where the Federation is open and bright, the Breen are secretive, closed-off and embrace the shadows.
Trapped on Draconica: Zarracka's is Daniar. They are sisters raised together and given equal blessing by Dronor, but Zarracka is vain and self-centered while Daniar is Modest Royalty and selfless.
From A Song of Ice and Fire, Ramsay Bolton is this to Jon Snow, despite the fact that they haven't even met yet* "Though an upcoming confrontation between the two has been foreshadowed.". Both of them are the bastards of Northern lords, but while Jon is heroic, Ramsay is a monster. Both of them were befriended by their trueborn brothers, the heir to their father's house, but Jon sincerely loves Rob while Ramsay is strongly implied to have murdered his brother. Also, while Jon adopts Tyrion's policy of admitting what he is so people can't use it to hurt him, Ramsay frequently forces people to refer to him as Lord Bolton's "trueborn heir," refusing to acknowledge his status as a bastard. Finally, in A Dance With Dragons, after his brother Rob's death, Jon rejects Stannis's offer to be made Lord of Winterfell instead opting to fulfill his duty's to the Night's Watch. Ramsay, on the other hand, sides with his father, rejects his duty to his lord and murders his way to become the current heir to Winterfell.
Their fathers Eddard Stark and Roose Bolton have a similar dynamic. The Starks and the Boltons could be considered this in general. While the Starks are the ancient rulers of the North, loyal and some of the most decent people in a Crapsack World, the Boltons are villainous traitors who murder Robb Stark and are rewarded with control of the North.
Artemis Fowl: Opal Koboi to the titular character. Both are rather arrogant masterminds who have taken an interest in each other's civilizations(Koboi with humans and science, Artemis with the Fairy world and Magic). Artemis is arrogant but ultimately a good person who comes to value his friends, while Koboi treats nearly everyone as a pawn.
In The Lord of the Rings, every good race has one twisted, corrupted counterpart. Orcs were once elves that were tortured and ruined. The Nazgul were once men. Trolls are these to Ents. The Balrog is an evil Maia. Gollum used to be a hobbit-like creature. In the film version, goblins are shown to be the twisted versions of dwarves. Goblin-Town even looks like a twisted version of the Dwarf Kingdom Erebor.
It works on an individual level, too: Saruman and the Balrog are each counterparts to Gandalf; the Witch-king and the other Nazgul are counterparts to Aragorn and the other human kings, Gollum is the counterpart of Frodo and Boromir is the counterpart of Faramir. Boromir, while not exactly evil, was more of an Anti-Hero, and his brother Faramir was able to resist the ring.
The Silmarillion has Morgoth and Manwe. Manwe is the King of the Valar. Morgoth began as Melkor, the most powerful Vala, but ends up as the Big Bad.
There are also Morgoth and Aule, which is lampshaded. Both enjoy creating new things, not always according to the will of Eru. However Aule created the Dwarves so he could pass his knowledge on, genuinely seemed to love them, and admitted his mistake to Eru Iluvatar, meaning the Dwarves were given true life. Morgoth's 'creations' are corrupted versions of pre-existing beings, such as the Orcs for Elves, treats them more as slaves, and Morgoth only pretends to repent.
In Cal Leandros, titular character Cal has Grimm. Both are human/Auphe hybrids, and share the same powers, attitude, and fashion sense. However, where Cal looks entirely human (save for his white skin), Grimm has the red eyes, white hair, and double row of retractable teeth of their Auphe ancestors. Also unlike Cal, who has spent most of his life trying to exterminate the Auphe, Grimm is trying to recreate the race.
Scourge is one for Firestar. Both were originally kittypets who ran away to the forest and became leaders. However, Scourge was brutally beaten and then chased off by a young Tigerstar, and went on to be the leader of a large gang in Twolegplace, while Firestar joined ThunderClan and eventually became leader. Their key difference is that Firestar has faith in his warrior ancestors and would die for his Clanmates, while Scourge treats those he rules over as mere pawns to be discarded when they've served their use. To highlight the evil counterpart-ness, Scourge was revealed to be Firestar's half brother.
Hawkfrost for Brambleclaw. Both are the sons of Tigerstar, but while Brambleclaw had to fight every step of the way to prove to his Clan that he was different from his father, Hawkfrost's parentage was a secret for a while and he had an easier path. And both are ambitious like their father, but while Brambleclaw is also loyal to his Clan and does not share his father's dark ideals, Hawkfrost devotes himself to following his father's ideals, and ultimately dies when he betrays all the Clans.
Spoilers for Crookedstar's Promise: Mapleshade is one for Spottedleaf. Both were involved in a forbidden relationship, but had to watch as their former loved one moved on from them and took another mate, this time in a relationship permitted by the code. Spottedleaf's love for Firestar was so great that she approved of his choice and cared for his loved ones and descendents like her own as a spirit. Mapleshade, however, was blinded by vengeance, and as a spirit she tried to corrupt and destroy the descendents of her former mate. Suddenly The Last Hopehaving Mapleshade be Spottedleaf's ultimate opponent makes perfect sense.
In The Elenium series, Martel is the counterpart to protagonist and Knight in Sour Armor Sparhawk; they were both raised as Pandion Knights and were renowned as the best of their order - equals in combat, intelligence and the use of magic. However, while Sparhawk retained unshakable loyalty to the order and his ruling monarch, Martel grew obsessed with personal power and delved into forbidden magic. He was eventually caught and excommunicated from the order, becoming a mercenary. At the climax of the Elenium they finally duel. Martel loses, and with his dying breaths admits he expected to.
Roland Marquis is this to James Bond in High Time to Kill. Both men are highly skilled professionals in their respective organizations and a have a history womanizing, but Bond is loyal to his government while Marquis had no problem selling out and become its enemy instead.
In Jack Schaefer's Shane Stark Wilson serves this role to Shane himself.
Piter De Vries from Dune is the Mentat assassin of House Harkonnen, making him the evil counterpart to Thufir Hawat, Mentat Master of Assassins to House Atreides. Thufir uses his abilities mainly to defend the Atreides, while Piter works mainly to destroy the Harkonnens' enemies (enjoying himself in the process).
In City of Heavenly Fire, the Jonathan Shadowhunter of the parallel Earth now known as Edom was this. Described as being a "divider", he apparently had some similarities to Valentine, and when the demons invaded his world in force, most of the Downworlders sided with them against that world's Shadowhunters, leading to the demons being victorious and the whole world being laid waste.
Mr. Thenardier and Jean Valjean are both ex-cons who hid their identities behind a facade of respectability (one is an honest politician, the other a thieving innkeeper). Valjean is religious, Thenardier is godless.
Mme. Thenardier and Fantine are both mothers but the latter is dedicated to her one daughter and the former treats her daughters like pets that she indulges as kids but maltreats when they grow older.
It's explicitly stated that Courfeyrac is the good counterpart of Tholomyes, the man who abandoned Fantine and Cosette.
In Please Don't Tell My Parents I Blew Up the Moon (sequel to Please Don't Tell My Parents I'm a Supervillain), retired superhero the Audit thinks that the Inscrutable Machine are deliberately mirroring her daughter and her friends out of jealousy. E-Claire looks enough like Claire that she probably heard variants of "Almost as pretty as Claire Lutra" a lot and her name is an obvious reference, Reviled's name is a reference to Ray Viles, and Bad Penny probably has a minor inventing ability that Penny's much stronger and more public one overshadowed. This is, of course, completely wrong. The real reason that the Inscrutable Machine looks and acts like Penny and her friends is because they are Penny and her friends. It helps that Claire has a minor shapeshifting ability that makes her look just different enough for the trick to work.
Avery Lazar to Lissa Dragomir in Blood Promise. Both are royals, spirit users, and have brought people Back from the Dead. But Lissa actually cares about people. Her shadow-kissed bondmate Rose is also her best friend. While Avery does not show real emotions. Her shadowkissed bondmates Reed Lazar (her brother) and Simon (her guardian) are little more than her slaves.
In various Michael Moorcock works, Gaynor the Damned (alias, in more technologically "modern" environments, Paul Van Minct) is the (in-universe identified) Chaotic Evil Evil Counterpart to every version of the Eternal Champion.