Jack - Stephen Saunders in Season 3, Christopher Henderson in Season 5, Tony Almeida in season 7, and Cheng Zhi in season 9.
In season 8 Jack becomes one to Cole Ortiz.
Michelle Dessler - Carrie Turner. She's not really bad but her ruthless effort to climb the ladder at CTU bordered on treason.
Karen Hayes - Miles Papasian
In Agent Carter,Dottie is this for Peggy. Both she and Peggy are secret agents, as well as skilled Action Girls. They both use other people's underestimations of their skill to their advantage. Peggy does this by using her coworkers' sexist assumptions about her abilities while Dottie does this by Obfuscating Stupidity and acting like a ditzy Country Mouse. Both are capable of flawless American Accents when undercover. They are also both Only Known by Their Nickname. But they use different fighting styles, with Dottie relying on She-Fu acrobatics, whereas Peggy relies on her fists, Improvised Weapons, and brute force. Additionally, Peggy chose to become a secret agent, while Dottie was Brainwashed into becoming a Child Soldier at a young age by her Russian trainers.
Buffy = Darla (bubblegum-blonde Honey Trap) and Faith (Slayer who became Drunk with Power. Whereas Kendra was the polar opposite of Buffy in nearly every way, Faith was meant to represent Buffy's "road not taken", a living embodiment of what Buffy might have been had her life's circumstances been different.)
Kumiko (evil Japanese sorceress who tried to wipe out the forces of good once and for all) = Willow (the most powerful witch in the world who even when she had gone dark did the wrong thing for the right reasons.)
Roden = Giles. The former hired a evil Slayer to kill Buffy, the latter hired Buffy's own Evil Counterpart in Faith to kill said Slayer and Roden.
Roden's evil slayer is this to Faith, who sees in the girl what she would be if not for her Heel–Face Turn.
Simone = Kennedy. One wants to kill Buffy for keeping Slayers defenseless before turning them into vampires, the other gives them the guns and training to be employed as guardians and offers Buffy and Faith high paying jobs.
Arrow. Oliver/The Arrow has several evil counterparts:
Malcolm Merlyn/The Dark Archer shares his goals in saving the city. Oliver tries to save the city by targeting the rich, while Merlyn targets the poor.
Slade Wilson/Deathstroke is a dark reflection of what Oliver was in the island.
In a dual example, Breaking Bad's final season gradually develops Todd Alquist and his uncle Jack Welker as the Evil Counterparts to Jesse Pinkman and Walter White, respectively. In addition to their individual similarities, Todd and Jack's relationship—with Todd clearly devoted to Jack as a surrogate father figure, and willing to do anything to please him—is very much a dark mirror of Jesse and Walt's relationship.
In contrast to Walt (an outwardly respectable man whose sympathetic motivations help obscure the odd horrific act that he commits), Jack is an unapologetically seamy White Supremacist thug who has the odd Pet the Dog moment amidst his long string of horrific acts.
In Brooklyn Nine-Nine, Jake has one in Doug Judy, aka the Pontiac Bandit: both are Bunny Ears Lawyers, both are often childish and frivolous, and they're shown to have near-identical interests and a shared love of role playing.
Captain Holt has two evil counterparts Deputy Chief Wuntch and FBI Agent Bob Anderson who both share his stoicism and hidden intensity.
Burn Notice. Michael has Psycho for Hire Larry, and Simon who will stop at nothing to take out everyone who (rightfully) burned him.
Some one episode villains can be this.
The Zamars from season 1 have the same dynamic as the Westens.
The medical scammers Todd, Philip and Rachel from season 2 are the bad versions of Sam, Michael and Fiona.
The Charmed Ones had the Demon Charmed Ones back in season 1.
And then there was the Mirror Universe miniarc, in which the Charmed Ones were harbingers of evil, and the demons were the good guys.
Chuck had his old flame Jill Roberts who was also a reluctant spy.
Sarah had Daniel Shaw because they both hide their passions behind a veneer of professionalism. As well as her former high school bully turned criminal Heather Chandler.
Stephen Bartowski and Alexei Volkoff both tested Intersect prototypes on themselves but the latter turned evil.
Morgan had Emmett Milbarge. They are both aware that they are in a dead end jobs at the Buy More but while Morgan (for a while) quit to follow his dream of being a chef, Emmett ruthlessly climbs the corporate ladder.
Many times in Cold Case the victim is killed by their evil counterpart.
City College and Dean Spreck to Greendale and Dean Pelton.
Annie Kim to Annie Edison in "Geography of Global Conflict". While both are ruthlessly competitive and Annie Kim might be better behaved than the prone-to-meltdowns Annie Edison, the former also lacks the humanising qualities that make the latter likeable and sympathetic despite her flaws.
The Monk, the first evil counterpart encountered. A similar rogue time traveller and renegade from the Doctor's planet, and owner of a much better TARDIS than the Doctor's - and a similar tourist in Earth's history. The difference is that the Monk is interested in using time travel to fiddle with TemporalParadoxes, pit historical villains against each other and try to accelerate human technological development, and lacks the Doctor's respect for history. The New Eighth Doctor Adventures from Big Finish Doctor Who develop this further - it is shown that the Eighth Doctor and the Meddling Monk consider each other the evil counterpart. The Doctor interferes with history to help people, but mostly will leave history intact and tries to find peaceful solutions, without killing innocents. The Monk tries to "improve" history and has a The Needs of the Many mentality, such as helping Ice Warriors take over Mars by killing thousands of human colonists to prevent the Ice Warriors killing billions when they attack another planet. This could be more emphasised in Big Finish by the fact that in his earliest Big Finish stories, the Doctor saving someone supposed to die nearly destroyed history.
The Master, the Doctor's Friendly Enemy and his equal in intelligence and madness. The main difference is that the Doctor is benevolent and the Master is not. Some incarnations are more and less direct counterparts than others - the Delgado, Ainley and Jacobi Masters are equals but with very different personalities to the Doctor, and the Pratt/Beevers and Roberts Masters go in Body Horror and Came Back Wrong directions first with their mirror nature secondary, but the incarnation of the Master played by John Simm is a very direct evil version of the Tenth Doctor specifically, inheriting a lot of Ten's personality quirks and tics.
Davros - one aligned with the Daleks and one with the Time Lords, both Mad Scientists, one works as a military "scientific advisor" while the other had worked as that and quit, both able to have complicated moral discussions with each other, and both - in "Genesis of the Daleks" at least - have a bit of Messianic Archetype or Dark Messiah about them, with Davros willing to create the Daleks and kill billions in order to become above the gods, contrasted to the Doctor's unwillingness to kill the Daleks and save billions because it isn't his right to do so.
The Valeyard in "Trial of a Time Lord", who turns out to be an actual Enemy Without of the Doctor embodying all of the actual and potential evil in his nature. Note that while the Doctor usually represents anarchic freedom, the Valeyard is obsessed with law.
in "Amy's Choice", the Dream Lord was a psychic manifestation of the darker parts of the Doctor's character, given life by psychic pollen that was stuck in the time rotor of the TARDIS.
In "Dragonfire", Kane is an ancient exile from his home culture who recruits alienated young women as his leading minions, and the main console in Iceworld's control room is similar in shape to the TARDIS's. However, he's utterly evil and abusively exploits his followers (by implication sexually as well). For a time in the story, he and the Doctor actually compete to win the loyalties of Ace, who becomes the Doctor's companion at the end.
In "The Greatest Show in the Galaxy", Captain Cook is presented as this for the Seventh Doctor — both are intergalactic travellers with a young, rather troubled companion and a bit of a manipulative, egotistical side, but where the Doctor is ultimately compassionate, brave and cares for both Ace and the people around him, Cook is callous, cowardly, selfish and abusive.
The Master's wife Lucy is in many ways a mirror image of Rose. Both are blonde women who fell in love with a Time Lord and became his loyal companion, but whereas Rose's travels with the Doctor seeing the wonders of the universe made her stronger and more idealistic, Lucy is a Straw Nihilist (thanks to being confronted with the horrible final remnants of the human race close to the heat-death of the universe) who can watch ten percent of the world die with a smile on her face and is utterly subordinate to her husband's will until she shoots him after seeing the end of the universe. Also, while the love between the Doctor and Rose was largely chaste and unrequited, the Master and Lucy's relationship is explicitly sexual and abusive.
In "The Tenth Planet", Mondas is the evil counterpart of Earth. Mondas looks exactly like Earth but flipped upside down, and the Mondasians are humans but forced to replace their bodies with spare parts, becoming the Cybermen, in order to survive as their planet drifted to the edge of the universe. They are now abominations with no emotions and the inability to comprehend human feelings, and get to win their ethical arguments anyway. However, the Cybermen lost this characterisation later to allow them to fill the Dalek-shaped hole left after the Daleks got Exiled from Continuity in the Troughton era, becoming generic nasty robotic aliens\a Dalek Suspiciously Similar Substitute race from "Tomb of the Cybermen" onwards.
In "The Time Warrior", Irongron and Linx seem to be a dark version of the Brigadier and the Doctor - a highly advanced and intelligent alien crash-lands his broken time ship on Earth, is discovered by a comparatively primitive and stupid military leader, and agrees to work for him and offer technology in exchange for board and the resources to fix his ship. The main difference is that the Brigadier is, while difficult at times, trying to selflessly defend his country from alien threats, while Irongron is a sociopathic warlord seeking personal power; and the Doctor is pacifistic and understanding while Linx is a Proud Warrior Race Guy and highly xenophobic.
Dr. Simeon from "The Snowmen" could be seen as a dark counterpart to Amy Pond: both encountered an extraterrestrial as children who made a huge impression on them. Whereas Amy grew as a person from her travels with the Doctor, Simeon was corrupted by the Great Intelligence, becoming callous and power-mad as an adult. Or rather, as it turns out, the Great Intelligence - very early in its timeline and learning by mimicry, becoming mostly a reflection of whoever it was connected to at that stage - was corrupted by him!Humans Are the Real Monsters indeed.
As a whole, the Time Lords have the Daleks as their evil counterparts. Note that this wasn't always true, but as the series drew on, it became more and more this way, before being cemented as such in the New Series.
Ditto in Elementary but with a twist: Moriarty is Irene Adler, who was Sherlock's girlfriend for a long time before faking her death in the most gruesome way possible.
Similar to the comic books, The Flash (2014) has Barry face off against villainous speedsters each season. In Season 1, it's the Reverse-Flash (Eobard Thawne/Harrison Wells); in Season 2, it's Zoom (Zolomon Hunter), as well as one-shot encounters with the Reverse-Flash and a female speedster named Trajectory. In Season 3, during the Flashpoint timeline, Kid Flash (Wally) has an evil counterpart in the face of the Rival (Edward Clariss), who may be building up to being Barry's counterpart in the main timeline, although there are indications that Zoom may have become the Black Flash and is using Clariss as a tool against Barry.
Ramsay Snow to Jon Snow. Both are the bastard son of a northern lord, but Jon is heroic and Ramsay is definitely not.
Ramsay's relationship with his father, Roose Bolton, is also a dark counterpoint to Jon's relationship with his father, Ned Stark. Where Ned loves and acknowledges Jon as one of his sons, raising him alongside his trueborn siblings in his castle, GRRM states in HBO's featurette 'Bastards in Westeros', "Ramsay gets nothing from Roose," with Roose treating Ramsay poorly and only acknowledging him when he has no other choice for an heir.
Joffrey Baratheon to Robb Stark. Both are young men who rise to power after their father's death and die by treachery at a wedding, but Joffrey is The Caligula and Robb is the Young Conqueror.
Glee has Santana, the Token Evil Teammate in the Glee club, who is a lesbian, a total bitch (and completely aware and proud of it), eager to sleep around, and freely enjoys screwing over her fellow club members' relationships For the Evulz... Come Season 3, this is somehow taken up a notch with Sebastian Smythe, who is gay, a dick, and instantly sets his sights on Blaine... He's also very much described as "a male Santana". In other words... he's the Evil Counterpart to the Glee Club's Token Evil Teammate. Yikes.
In season 4 of Haven, Duke Crocker gains one in his brother Wade. Both have the same Trouble, the ability to absorb blood to gain temporary Super Strength and the ability to completely erase a Trouble by killing one person who has it. When Duke discovers his Trouble, he resolves to only use it to help others, like when he absorbs blood from a woman's wound to become strong enough to free her from her crashed car, and only kills to defend himself or others. When Wade discovers his Trouble, he quickly becomes a Serial Killer, killing for no higher purpose than absorbing blood and getting high off the rush of strength. Their late father Simon was much like Wade, making him a posthumous evil counterpart to Duke.
Heroes gives us Peter Petrelli and his evil counterpart Sylar. Both wanted to be special, both are initially believed to be powerless at first, both have absorbing powers, and both want to do great things with their powers. Peter comes from a wealthy amoral family who view him as the underachiever, while Sylar comes from a poor religious power family. Peter goes against his family's wishes to pursue a career in nursing to help people, while Sylar becomes a watchmaker to appease his mother. Peter desires to be special, but he ultimately wants to use it to help people, while Sylar let is desire to be special to consume him and lead him to murder, manipulations, sadism, etc. Sylar initially kills people to steal their powers, while Peter absorbs people's powers by empathizing with them. As the series went on Peter and Sylar's stories always paralleled with each other. Part of the third season explored similarities and difference between them and how easily Peter could have become like Sylar or Sylar become like Peter.
The entire town of New Bern is this to Jericho. Jericho is a peaceful salt mining town. New Bern is under martial law and run by the sheriff. Their main export is gunpowder. White vs. black, get it?
Kamen Rider also frequently makes use of this trope. Most of the time the Evil Counterpart is another Rider who is essentially a Palette Swap of the original. If not, he still functions largely the same as the original. The earliest known example of this trope in Kamen Rider are the Shocker Riders in the first series.
Leverage has a number of counterparts to the main characters, although not all of them can be strictly called evil. A less ambiguous example is Chaos, a hacker of almost equal skill to Hardisson but completely lacking in ethics (in his first appearance, he tries to kill his entire crew to make off with the money). There's also Sterling who is just as smart as Nate (they used to be friends). The kick is, Sterling is actually working within the law (he even becomes an Interpol agent), while Nate constantly breaks them.
Merlin has Merlin and Morgana, each fighting for the rights of magic-users, each on different sides.
First, there was Cora, who as Regina's mother also practices magic and does horrible things to the people around her. However, while Regina's love for Henry is a speck of light in her darkness for which she began to redeem herself, Cora only got worse as time went on, corrupting and killing like no other.
Next, there was Peter Pan, a contrast to Rumplestiltskin.
After that, it was Zelena, Wicked Witch of the West, who contrasted with her half sister regina in how much the latter has changed.
Lilith is introduced as this for Emma though the through extent of her evil and Emma's good has yet to be seen.
The Snow Queen was this to Elsa.
Inverted with Merlin, who received his powers the same way as the Dark One, and can be controlled by Excalibur, but uses his powers for good, not evil.
In Person of Interest, counterparts (evil or not) are a recurring theme, and most of the main characters have more than one. Listing just the evil examples, though:
Finch has several evil counterparts, reflecting different aspects of him: Root before her Heel–Faith Turn (a super-hacker who erased her own identity and has cultivated a unique relationship with the Machine); Carl Elias, the mob boss (a mild-mannered, bespectacled man who hides in the shadows and is secretly a master manipulator and criminal genius whose will is enacted by his mysterious companion); and Greer (leader of a rival group to the Machine gang, albeit following the edicts of Samaritan, which is in turn the Machine's Evil Counterpart).
The Machine has Samaritan, a rival AI which, instead of being taught restraint, empathy, and respect for free will, instead directs its followers to kill targets, believes itself to be a god, and generally acts like a spoiled child with limitless power.
Reese has his former partner Kara Stanton, and Elias' right hand man Scarface, as well as the various ex-special forces/intelligence assassins he runs into.
Fusco's counterpart is Simmons.
Martine is simultaneously the Evil Counterpart to Shaw (emotionless, lacks empathy, states that all her interests revolve around guns) and Root (constantly in God Mode - i.e. following the instructions that her AI overlord whispers in her ear).
Scandal: Huck discovers that his girlfriend Becky is this for him. They are both super-spies, they have the same skill sets, and they have both done their share of dirty business. However, Huck has a conscience and friends, while Becky is heartless and a loner.
A two-part episode of The Sentinel introduces Alex Barnes, who has the same hyperactive senses as Jim but turns out to be a Classy Cat-Burglar. She's also willing to kill anyone who stands in her way, even someone who helped her get a handle on her abilities. She ends up finding an ancient Peruvian temple and performs a ritual that temporarily boosts her abilities Up to Eleven, but this ends up frying her brain.
Sherlock has a particularly fascinating version of one of the oldest of these pairs: Sherlock Holmes and Jim Moriarty.
Bizarro, General Zod, and his Kryptonian stooges also make requisite appearances.
Lionel Luthor is patterned as a dark mirror to Jonathan Kent. Both died, but one expired by natural causes while the other got shoved out a window by his kin. Whoops.
In season nine of Stargate SG-1, the Ancients were discovered to have been holding another group of ascended beings called the Ori at bay for tens of thousands of years. The Ori have all the reality warping powers of the Ancients and none of their (questionable) ethics, having discovered a way to harness lowers' worship to increase their own powers.
The Asgard are the good counterpart of the Goa'uld, Sufficiently Advanced Aliens seen as gods by the humans of the worlds they lead, but the Asgard protect their charges instead of enslaving them.
Stargate AtlantisSeries/''. Kolya is in may ways a counterpart to John Sheppard. Both are extraordinary soldiers, both command incredible loyalty from their men, and both have made difficult choices for the good of their people. Kolya just happens to also be an amoral bastard.
The Star Trek Mirror Universe is populated by shadow selves and outright evil counterparts of people in the standard universe.
In the TNG two-parter "Chain of Command", Picard is grilled by an interrogator who shares his interest in books and archeology. Most of it is a mind game, of course, but at one point the Gul expresses hope that the two of them can debate philosophy sometime. (Not likely.)
Ben Sisko's archrival on Star Trek: Deep Space Nine, Gul Dukat. Dukat once ran Deep Space Nine as a shogun-style warlord, but was deposed by the people he tried to subjugate. On his arrival, Sisko is hailed as the messiah to that planet's inhabitants. D'oh. Later, Dukat is made the Emissary to the Pah-Wraiths, evil aliens standing in opposition to Sisko's benefactors, the Prophets.
The Dominion was designed to be an anti-Federation, rather than a single hostile alien race like other antagonist factions. Like the Federation, the Dominion was made up of hundreds of races and thousands of worlds, but bound togetehr by fear and enforced obedience rather than idealism.
The U.S.S. Voyager came across a rogue Starfleet vessel, the Equinox, which had been using sentient beings as fuel to get home faster. Amusingly, their EMH has had his ethical subroutines removed, making him a full-on Evil Twin of The Doctor.
Lucifer and Michael are evil counterparts to Sam and Dean. Gabriel notes that Sam and Dean being Michael and Lucifer's true vessels is quite fitting, as both Dean and Michael are eternally loyal to their absent fathers, and both Sam and Lucifer constantly rebelled against their father's plan.
Super Sentai and Power Rangers have had several evil counterpart teams to the Rangers, though the evil team most people remember are the ones in Denji Sentai Megaranger and Power Rangers in Space, the Nejirangers/Psycho Rangers respectively, who actually named a subtrope: The Psycho Rangers. However, there are also episodes in which only one of the Rangers gets an evil counterpart, thus playing this trope straight, rather than the subtrope. Examples are:
Gosei Sentai Dairanger has Tetsumenpi Chouryuo; an armored warrior capable of using the same techniques the Dairangers can.
Zeta Zeta Psi and Kappa Kappa Phi, the two sororities featured on Sweet/Vicious, are as diametrically opposed to one another as can be. While the Zetas are all about sisterhood and female empowerment, making their pledges feel welcome through mutual support, the Kappas are a bunch of vicious alpha bitches who abuse and haze their pledges to the point of sexual assault and hospitalization. When Kennedy, the leader of the Zetas, tells the new pledges "welcome to Hell Week", she's pretty obviously being sarcastic about it, while Chloe, the leader of the Kappas, is dead serious when she describes her sorority's Initiation Ceremony with those words.
From Tower Prep, the Rook leader in episode five is this to Ian, right down to the same power.
The Transporter in the season 2 episode entitled T2 introduced an evil counterpart for Frank Martin named Olivier Dassin. Like Martin he is a professional transporter but is more ruthless, treacherous, and essentially on the whole lacks Frank's moral compass.
MacPherson to Artie in Warehouse 13. They used to be partners and friends until both fell in love with the same woman. The break happened when the woman was trapped in a burning building, and Artie refused to ues the Phoenix, an artifact that would allow one to survive being burned but would kill a random person instead. MacPherson used the Phoenix to save her and was kicked out of the Warehouse. He has since spent years tracking down artifacts, like Artie. However, he doesn't want to put them away for safekeeping but to use them to further his own ends. He even has a Tesla of his own.
Brother Adrian is the head of the Brotherhood of the Black Diamond, a Vatican-based organization dedicated to keeping dangerous artifacts safe. Sound familiar? After Artie steals Magellan's Astrolabe from Brother Adrian to prevent the destruction of the Warehouse, Brother Adrian shows up and demands that Artie use the Astrolabe to revert his changes and starts to dismantle Artie's life's work with his own artifacts. Subverted in the end, though, when it's revealed that Brother Adrian never came to the Warehouse, and it was Artie's split personality who was doing the stealing and the killing, resulting in Leena's death.
Paracelsus to Claudia in Season 4. Like Claudia, Paracelsus is a scientist (of the mad kind) and likes to experiment with artifacts to find out how to use them better. It was his research that enabled safe bronzing of dangerous individuals (in a twist of irony, he became one of the first to be bronzed). However, Claudia is not willing to risk people's lives for her research, and Paracelsus most definitely is (he simply calls them casualties of progress). Paracelsus is also revealed to have been the Caretaker of Warehouse 9, a position that Mrs. Frederic holds in Warehouse 13. Claudia is being groomed as the next Caretaker. The finale of season 4 has Paracelsus taking control of the Warehouse and kicking everybody out, except for Claudia who stays behind to battle him.
In The Wire, Cheese is this to D'Angelo. Cheese is also the nephew of a drug lord. Despite the way he looks, he's a Dirty Coward. Dee stops trusting his own family but never snitches on them. Cheese openly brags about betraying his uncle to his death and gets killed for it.
Another episode has a Russian sniper named Yuri whom Blair even calls Jim's technological counterpart. Both have military training. While Jim uses his natural hypersenses, Yuri uses technology (e.g. binoculars, sniper scopes, heat sensors) to achieve the same level of awareness. They also previously tangled during Jim's military days, where Yuri outmaneuvered Jim's squad and killed the man they were supposed to protect.