The 1950s incarnation of Captain America ("Commie Smasher") was (through the magic of Retcon) explained away as an obsessed fan of the original who insisted on replacing him during the time when he was presumed dead; while the US government decided to humor him, the faulty version of the Super Soldier enhancement process eventually drove him insane. While he was eventually captured and placed in suspended animation, he broke out years later and attacked who he thought was another Captain America imposter - the real Captain America, who had defrosted from his own accidental suspended animation.
There was also Protocide, a test subject for the Super Soldier serum who went crazy with pain, got put in storage for many years, then was let out by AIM and manipulated into going after Steve Rogers. There was some 'opposite' motifs going on in his appearance: his costume was red instead of blue, and he had a far pointier shield.
He and The Falcon briefly had an enemy named Anti-Cap, who was meant to be a modern day Deconstruction of Captain America with the World War 2 background swapped out for a more timely War On Terror one. He even wore a black variant of the Captain America costume.
To really hammer home the counterpoint, Anti-Cap was a Navy man.
Black Adam was the Evil Counterpart of Captain Marvel, his predecessor as a bearer of the power of Shazam who became corrupted by its power.
Carol Danvers has Doctor Minerva, a Kree scientist who gave herself the same powers as Carol and even wears a variation of her old costume.
Also Moonstone, who even posed as Ms. Marvel for a time during Dark Reign.
Similarly, not only was the Green Lantern foe Sinestro once a Green Lantern himself, in Post-Crisis continuity he actually trained Hal Jordan in the use of his powers before becoming his nemesis.
In more recent times, there are even more popping up, but not all evil (so sort of non-evil counterparts to the evil counterparts): while the green represents will, and yellow represents fear, there's now violet (love), blue (hope), red (rage), orange (greed), and indigo (compassion). And eventually black (death), which is the really evil counterpart.
The White Lanterns are a Good Counterpart to the Black Lanterns, as both are Corps that resurrect and recruit the deceased. The difference is that the Black Lantern Corps essentially raises its recruits as zombies that feed off emotions and are used by Nekron to further his plan of killing all life, whereas the White Lanterns are resurrected properly and are recruited to repair the damages done by the Black Lanterns.
Kyle Rayner got 2 energy-wielding/manipulating Evil Counterparts, himself. On the 'ring-wielder' side of things, Alex Nero - who was Ax-Crazy, and possibly killed his parents as a teenager. On the 'might've become' side of things, Effigy, who was what Kyle might've been if he hadn't matured and gained a sense of responsibility about the ring and super-heroics in general.
Some individual members of the Sinestro Corps are evil counterparts of specific GLs; for instance Arkillo (Evil Kiliwog) and Ranxx the Sentient City (Evil Mogo the Living Planet).
The criminal Killer Moth originally patterned himself as an Evil Counterpart to Batman... but quickly sank to a third-string position in the Rogues Gallery. As we said, the Counterpart is sometimes a Big Bad, but not always. It was probably a bad idea to name himself after something bats eat.
Continuing in that vein, the Wrath was a Pre Crisis villain who was even more of a Batman counterpart, down to duplicating much of his origin (his parents being killed in a shootout by Commissioner Gordon in his days as a rookie beat cop). Not only did he not become a Big Bad, he was essentially a one-shot opponent.
The Joker briefly had his own sidekick named Gaggy, who like Robin, was a former circus acrobat. He never caught on, but returned decades later as an enemy of Harley Quinn and the Gotham City Sirens.
And similarly, Batman Confidential introduces a new Wrath, the original's protégé, as Nightwing's foe. He proved to have more staying power than his predecessor and later stepped up to Batman himself as the Big Bad of Detective Comics for a time.
And both Prometheus and the Wrath are at large once again. Yes, they're practically the same person except for Prometheus' focus on technological gadgetry.
Bane was created as something of an Evil Counterpart to Batman, having trained his mind and body while in prison (serving part of his late father's term). The big difference is Bane's use of the chemical Venom to give himself Super Strength. Bane could also be considered an evil counterpart to Doc Savage, particularly with regard to his original aides.
Two-Face also mirrors Batman in his dual nature - Batman's identities are secret and united in their goals while Two-Face's are obvious and opposed. Harvey Dent started out with the exact same goal as Bruce, making him an example of what Batman could become if he loses his self-control, and was a close friend and confidant of either Bruce or Batman in most continuities.
While Bruce Wayne had caring, loving parents, Tommy Elliot's were both cut from the Rich Bitch cloth (and his father was an abusive alcoholic). To keep himself from harm and create a better life for himself, he arranged a car accident that killed his father and left his mother an overbearing cripple. Tommy hated that Bruce's dad saved his mom and that Bruce eventually got the life Tommy wanted for himself. Upon being told by the Riddler that Bruce was Batman, Tommy became Hush, an archetype of Batman who is a criminal mastermind.
Owlman and Talon, Batman and Robin's counterparts from Earth-3, the Evil Counterpart Universe.
The Ax-Crazy Black Mask. Like Bruce, he was the son of wealthy parents who died due to unnatural causes. The difference is that Black Mask happened to kill his own parents and run his company into the ground with his own incompetence, before becoming a masked and increasingly violent crime lord. He even met Bruce as a child. He's as much of an Anti-Bruce Wayne as an Anti-Batman.
Catman was going to be one of these for about 5 minutes. Add in the Red Hood (formerly Jason Todd, the 2nd Robin, a vigilante who kills villains left and right when he isn't in Countdown) and Batzarro, which, yes, is a thing that really exists, and he has about a dozen of these.
Deadshot is still another example, the son of a wealthy Gotham family, a Rich Idiot with No Day Job by day and a Bad Ass Normal by night. The primary differences in his life from Bruce's are that he attempted to stop the tragedy as it happened, but his Abusive Parents survived while Deadshot accidentally killed his beloved brother. Already The Unfavorite with both parents, Deadshot initially took to vigilantism and crime out of boredom, before graduating to both Blood Knight and Death Seeker. Batman, in contrast, began his career out of a compulsion to serve justice and later developed a stronger desire to ensure that Everybody Lives.
Batman's gallery is built on the Evil Counterpart concept, mainly because writers acknowledge that what Bruce does isn't exactly sane and love to point out how easily it could have gone another way.
To the point where its hard to find a villain who isn't an evil counterpart of some facet of Batman. The Joker himself has pointed out they are both the results of something traumatic and life shattering (maybe), but to add, the Scarecrow uses fear just as much as Batman does, the Riddler uses his intellect more effectively than physical strength, Ra's Al Ghul is a man with a lifelong war on crime, and Mr. Freeze is motivated into his actions by the person he loves most in the world.
In Death Of The Family, while The Joker has always been this to Batman, this time he is figuratively borrowing pages from Batman's book, like turning off the lights to get the drop on a group of his enemies, and finding out the Batfamily's secrets so he can hit his enemies where it hurts!
Dr. Hurt is Thomas, and to a lesser extent, Bruce Wayne's evil counterpart, using his wealth and influence for evil.
James Gordon Jr. was described by Scott Snyder as the exact opposite of everything his father stood for.
Jean-Paul Valley's take on Batman, especially when he reaches the pinnacle of his Sanity Slippage, is easily this - a Batman who wears flashy armor, armed to the teeth with deadly weaponry and finally ready to spill blood.
As he was originally a Fantastic Four supporting character, one could argue Black Panther is the Good Counterpart of Doctor Doom. Both men are costumed, superpowered rulers of advanced high-tech nations with ties to the FF.
In-story, Storm claims that Black Panther and Magneto mirror each other in many ways, though they aren't really enemies.
Venom is Spider-Man's Evil Counterpart, created when he symbolically cast off the darkness within him. Later, when Venom became an Anti-Hero, Carnage was created to be his Evil Counterpart. Years later, Eddie Brock became Anti-Venom and was the Good Counterpart to the third Venom.
Toxin is Venom's Good Counterpart.
The tables have been turned on that one, Eddie Brock is now Toxin, and now Flash Thompson, the current Venom, is Eddie's Good Counterpart.
Spider-Man has had several villains meant to be his thematic opposite, from the Fly (who gained his powers in an accident much like Peter's own, but never stopped "looking out for number one" and blamed everyone else for his shortcomings) to the Scorpion (ditto; Bonus points for being an arachnid, too. And then the original Scorpion became Venom for a while). Dr. Octopus shares many personality traits with Spider-Man and is even based on another 8-legged creature. Less obviously, there's the Spider-Wasp.
And The Thousand, an old schoolmate of Peter's who witnessed the accident that turned him into Spider-Man. He went back to the lab after hours, found the dead spider, and ate it. It turned him into a being capable of becoming a living swarm of spiders. He ended a promising criminal career as a single very ambitious spider who failed to notice a large human foot coming down behind him...and—squash.
Joe Straczynski's run has Ezekiel, through not that evil — he is quite good-intentioned but lacks Peter's heroic qualities (through Peter inspires him to some acts of heroism at one point or two). They have the same powers, but while Peter got his by accident, Ezekiel actively sought them because he couldn't live with feeling powerless. While Peter sacrifices his well-being to help people as superhero, Ezekiel uses his powers for personal gain. While Peter never let anything gets in his way of helping people, Ezekiel always hides behind excuses, when he could be a hero. When having to suffer consequences of their respective actions, Peter accepts them while Ezekiel tries to trick him into taking his place. In the end Ezekiel has a Heel Realisation and makes a Heroic Sacrifice to save Peter after their minds merged for a moment and an exchange of memories occured.
Another one from the same run is Charlie Weiderman — he was a nerd picked upon through high-school just like Peter, but grew up harboring grudges, while Peter not only forgave but befriended his high-school bully, Flash Thompson. When Charlie gets powers, by accident, he immediately goes to exact revenge on anybody who wronged him.
Sabretooth is portrayed as Wolverine's evil similar, with near identical powers and completely feral. And he's implied to be Wolverine's half-brother; if he is, then they've hated each other their entire lives. Interestingly however, both characters were introduced separately from each other, Wolverine first appeared (with slightly different powers than his X-Men debut) in the Hulk comic, while Sabretooth was introduced (with no powers at all and claws that were only part of his gloves) in the pages of Iron Fist.
This may not be quite so coincidental, as Chris Claremont and John Byrne were working on the Iron Fist title around the same time as their classic run on X-Men.
Wolverine's enemy Silver Samurai has an inversion of this with Ebon Samurai. Word of God states that Ebon Samurai was a police officer that was killed by Silver Samurai, only to be resurrected as a vengeance-driven superhero.
Wolverine's Rogues Gallery is filled with long-lived mutants with healing factors, claws, and/or adamantium. Let's see we've got: Cyber, Lady Deathstrike, Romulus, Daken, and Omega Red.
Following in their dad's footsteps, X-23 and Daken seem to be heading towards this type of relationship with X-23 being the "good" counterpart and Daken being the "evil" counterpart.
Flintheart Glomgold, of the Disney Ducks Comic Universe (and later DuckTales) is an evil counterpart to Scrooge McDuck - every bit as ambitious as Scrooge, almost as wealthy, but with none of Scrooge's redeeming factors, such as his honesty and sense of fair play.
DuckTales even increased the similarities by making Flintheart Scottish, the same nationality as Scrooge - though this was because he was originally South African in the comics, and they wanted to avoid unfortunate connections.
Blackheart Beagle is another Evil Counterpart, ambitious like Scrooge, the head of a large family like Scrooge, cares about his family like Scrooge, and a Badass Grandpa like Scrooge, however he tries to steal money instead of earning it.
The Marvel Comics series Sleepwalker has an Evil Counterpart in Psyko, who possesses warping abilities similar to Sleepwalker's. Sleepwalker, an alien devoted to protecting the minds of innocent people from insanity, became fused with the human Rick Sheridan when he found himself trapped in Rick's mind, whereas Psyko was created when a human Serial Killer became fused with a demonic creature from the Mindscape, giving him the ability to spread his madness like a disease, Mind Raping everyone around him.
Other than their common teacher, however, the two men actually do not have very much in common, their life histories and backgrounds are very different. Doctor Strange did not even realize the supernatural was real until his middle years, and only began to pursue it because an accident crippled his surgical abilities, his background is actually scientific. Mordo was raised supernatural, from a supernatural family, and steeped in evil from early youth, his background is more traditionally magical/occultist, and he always sought power.
The Catwoman series tried giving Selina an Evil Counterpart a couple of times. One was She-Cat (another cat-based thief, but a less skilled and less ethical one, who eventually turned out to know Selina from when they were in the same orphanage) and another was Hellhound (a male chauvinist who'd been trained by the same Old Master, and been The Unfavorite). Neither of them caught on.
Aquaman has had several evil counterparts. The most obvious is the Ocean Master, his own brother. Others include Charybdis, Evil Twin Thanatos, and the Thirst.
In Circle of Blood, the first miniseries for The Punisher, Castle fights against a brainwashed army of criminals, all patterned after him.
Judge Dredd has the Dark Judges, who have taken the policing style of the Judges to an extreme where Mega-City One is practically Utopian. Their world has indeed become devoid of crime. It has also become devoid of life.
The Mandarin is more the anti-Stark than the anti-Iron Man. Stark is a thrill-seeker. Mandarin participates in gladiatorial games so he can thrill to putting his fist through someone's head. Stark sacrificed his health so he could help the world. The Mandarin sacrifices everything and everyone around him to become stronger.
The various Crimson Dynamos and Titanium Men were originally created to be Communist (and therefore, at the time) Evil Counterparts to Iron Man. Since The Great Politics Mess-Up, they tend to get played more as the rival or even the Worthy Opponent.
Justin Hammer is the anti-Stark-as-businessman. While Tony uses his money to fight crime, Hammer uses his to sponsor it.
The Hulk now has the Red Hulk. The Leader and the Abomination probably fit this role too.
Oddly enough, Hulk's Rogues Gallery also includes someone else's Evil Counterparts. The U-Foes are a group of four villains whose origin, powers, and personalities are all extremely similar to those of the Fantastic Four. Strangely, they have never faced the FF despite all of the characters being Marvel Comics characters.
Titania too. Like Jennifer, she was also a shy wallflower in high school that gained superpowers later in life. There are a few key differences though. She-Hulk never asked for her powers (she adjusted well enough though) while Titania was so desperate to be powerful and special that she let Doctor Doom experiment on her. She-Hulk's transformation helped her gain real confidence both as She-Hulk and as Jennifer Walters. Titania's powers act as a crutch and deep down she is still the insecure Mary MacPherran. Titania resents She-Hulk specifically because She-Hulk is stronger than her in every way.
"Except for an accident of circumstance, I could have been your Luke Skywalker, and he could have been me. After all, we were both farmboys who loved to fly." Baron Soontir Fel, the best non-Vader pilot in the Empire, says this to Wedge Antilles after he's captured by Rogue Squadron. Farm Boy origins aside, he's actually closer to being the counterpart to Wedge, who also happens to be his brother-in-law. Fel is distinctly not evil; he's Imperial, which does put him on the "wrong" side, but he's not an evil man. He actually joins Rogue Squadron for a time, before disappearing and ending up as part of the Empire of the Hand.
Moon Knight had Evil Counterpart villains for his Marc Spector identity (Bushman), his Steven Grant identity (Midnight Man), and his Moon Knight persona (Black Spectre).
At the end of Warren Ellis and Decan Shavley run new Black Spectre was introduced, being this for their reimagining of Moon Knight. His introductory issue is all about how he pretty much redefines himself to be this for Moon Knight.
Starman's Jack Knight and Nash were on their respective sides of the law mainly because their fathers pushed them there.
All four Flashes have fought a "reverse flash" of some sort or another. Jay Garrick had the Rival, an old college professor who discovered his power source and committed crimes dressed like the Flash. Barry Allen fought Professor Zoom, a stalker who wanted to destroy everything Flash loved. Wally West's counterpart is Zoom, a former profiler who is convinced that super heroes are only effective if they lose people they care about. Bart Allen had Inertia, an evil clone of himself.
Barry Allen also fought his prior to unknown twin Malcolm Thawne aka Colbalt Blue who established his own legacy of evil that mirrored the Flash Family. Including Professor Zoom.
The New 52 gives Barry another Reverse Flash; Daniel West, the younger brother of his love interest Iris. Taking the parallel further, he was a criminal before becoming the Reverse Flash, in contrast to Barry's role as a cop.
From the Knights of the Old Republic comics, both Big Bad Haazen and hero Zayne Carrick are relatively weak Force-sensitives who were considered failed Jedi apprentices. The difference is that Haazen allowed his bitterness and jealousy of his more talented peers to utterly consume his life, while Zayne still maintains his fundamental human decency no matter what. The series' other main protagonist, Jarael, now has one of her own in the form of Chantique, who represents what Jarael would be if she allowed herself to be dominated by her Dark and Troubled Past.
Raven Red in the Jet Dream feature. Like Jet, she's also a top-notch aviatrix with an all-girl team.
Reed Richards and Doctor Doom: archenemies, both intellectually-inclined supergeniuses, both master inventors, both with major strengths in technology, both hammy and prone to Sesquipedalian Loquaciousness, both pretty similar in personality once you factor out Doom's This Is Your Brain on Evil. A lot of their battles consist of them passive-aggressively complimenting each other's moves in ways that often sound a lot like two computer geeks playing together. The key difference between them usually centres on how they handle responsibility; Doom's entire motivation stems from the fact that he can't accept that it was his own error, not Reed's interference, that caused the accident which scarred him, and maintains his vendetta to avoid having to acknowledge that he was at fault all along and Reed is just a little bit smarter than him, while Reed is a lot more willing to accept fault when he's in the wrong and will attempt to make amends or correct his mistakes.
Doom is sometimes also used as an Evil Counterpart to Iron Man: both battlesuit wearing geniuses with serious character flaws.
The All-Purpose Power Tool itself has an Evil Counterpart in Ironarm's Worldbeater, a massive, polluting contraption with bolted-on components that tears up the landscape as it works.
Death Mayhew, commander of the Nazi flying group the White Lions, was this to Blackhawk.
While they never met, Kevin and Miho from Sin City were meant to be counterparts of one another. They're both improbably strong and neither ever speaks. Kevin is obviously the evil one while Miho is at least the Anti-Hero version.
Marv and Manute from the same series also fit as they are both big, scary determinators. Dwight all but lampshaded this when he brought Marv in to deal with Manute. Bonus points are given to the fact that while Manute is evil, well dressed, and highly educated, Marv is good (in comparison), a bit of a bum, and not very book smart.
In a way, Gideon Graves to Scott Pilgrim. They are initially pretty opposite as Gideon is a successful multi-millionaire mogul whom is viewed as a winner while Scott is seen as a lovable loser. Both have large combat experience, with Scott being the fighter in the province and Gideon inventing the Glow for military purposes. However, Gideon serves as a darker form of Scott or rather who Scott may end up becoming (being 7 years older than Scott.) Both tend to be uanware of their misdeeds (though Scott never explicitly denied his Gideon interfered with his memories to some extent and both can be bad people to their girlfriends. However, Gideon is much worse than Scott and Scott's realizing they are alike in ways allows him to unlock the Power of Understanding.
Nancy Thompson has become Freddy Krueger's good counterpart in Nightmares on Elm Street, as she has developed dream powers of her own that she uses to help people. Unfortunately, she hasn't fully accustomed to the dream world and lacks the years of experience that Freddy has.
The Beano has Pa Bear and Grizzly Gus two bears who love food in a strip called The Three Bears. The Dandy's most iconic strip Desperate Dan has Dangerous Dan Mc Groo who looks almost exactly like Desperate Dan, albeit in a more evil costume.
Red-Mist is this to Kick-Ass. While Dave was inspired by the heroes in the comics, Chris was inspired by the villains (even quoting The Joker before setting up his Avenging the Villain story-line in Volume Two).
In the Archie Comics' Sonic the Hedgehog series, Sonic has a direct evil counterpart in the form of Scourge the Hedgehog. Unlike Shadow, who often acts as a foil to Sonic, and Metal Sonic, which is a robot built to serve Dr. Eggman's diabolical purposes, Scourge is literally an evil counterpart: He is Sonic from a parallel dimension, where the protagonists and villains switch roles. In the early days of the comic, Scourge was simply known as "Anti-Sonic" and was identical to Sonic save for sunglasses, a black leather jacket, and a Jerk Ass attitude. More recently, Scourge has differentiated himself with a new moniker, a new green color, and a personality that is much, much more malicious than before.
He, then, forces this on his Anti-Freedom Fighters, turning them into the Suppression Squad and even they just as bad. Princess Sally's counterpart, Alicia, is nothing more than a figurehead. Miles, Tails' counterpart, is cold, calculating and the real brains behind the team. Rotor's counterpart, Boomer, took his genius and used it on himself, turning himself into a cybernetic terror (which also makes him Bunnie's evil counterpart, as her counterpart, Buns, ends up becoming E-123 Omega's... not-so-destructive(?) counterpart). And Patch, Antoine's evil counterpart, is completely vain and in it for power.
Tabby Brennan was set up to be this to the Huntress, in that both were the daughters of powerful crime bosses, and both schemed to murder their fathers under the noses of several superheroes. The difference is that Santo Cassamento hated Huntress, and was trying to force her into the mob as his personal enforcer and assassin, while Tabby's father loved her and was trying to quit his life of crime for her sake; Huntress killed Cassamento to get out of the mob (and for revenge), while Tabby killed her father to take over his gang. Lampshaded when Huntress thinks of Tabby as "Just like me." Of course, then Tabby got killed off in a really stupid manner, but the less said of that, the better.
Captain Atom has the Ghost, a.k.a. Alec Rois, a.k.a. the Faceless One. Both men died and returned with quantum-powers, but whereas Captain Atom returned as a living being, Rois came back as, well, a ghost. Their powers cancel each other out, and Cap is a hero while the Faceless One is a villain. Both are manipulated by Wade Eiling, despite being excellent strategists and intriguers themselves.
There is also Major Force, a criminal named Clifford Zmeck who was given powers similar to Nathaniel Adam's in exchange for being pardoned for his crimes.
Axis Amerika was this to the All-Star Squadron, ironically modeled after the Golden Age/Earth-2 heroes (namely, Superman, Batman, Robin, Wonder Woman, Aquaman, Green Arrow, and Speedy) who vanished after the Crisis on Infinite Earths, with the only exception being Kamikaze, who simply was Imperial Japan's replacement for Tsunami. They soon meet their match with the Young All-Stars, who filled the shoes of the erased All-Stars. Before that, there was Der Zyklon, who was a Nazi super-speedster counterpart of the Flash and Johnny Quick.
Daredevil has Ikari, a ninja-themed warrior who has the same powers as Matt but with the added bonus of not being blind. Also whereas Daredevil is more of a Fragile Speedster, Ikari is an Implacable Man.
In many ways Hawkman villain Gentleman Ghost is Hawkman's opposite. Where Hawkman is a powerful Boisterous Bruiser with a love of fighting, Gentleman Ghost is a laidback Affably Evil chessmaster who prefers to manipulate people. Also they both use magic but where Hawkman uses magic to add to his formidable power, Gentleman Ghost prefers more creative uses such as invisibility or teleportation.
In the Fables universe, Dorothy Gale is this to Fabletown's Cinderella. They're both female, attractive, and work black ops...but Dorothy works freelance, purely for money, while Cindy considers herself a Fabletown patriot. They are blood enemies.
In Thunderworld #1, in the Sivannas of the Multiverse, there's a Hannibal Lecter-esque version who is far more bloodthirsty and depraved than the rest of them, who travelled back in time and violently murdered his universes' Billy Batson before he became the Wizard's champion, and as a result has become very bored.
In the Marvel universe, the Masters of Evil are essentially the supervillain equivalent of The Avengers and have existed for almost as long. Their roaster is very large and constantly rotating but has several core members, just like their heroic counterparts. Just about every professional supercrook worth their salt has been at least partly allied with the Masters at least once and being a member is considered by some villains to be a badge of honor. In fact the Masters were originally founded with this trope in mind; Baron Zemo realized that the Avengers were doing so great partly because they were working together as one big organization and decided that if the bad guys could do the same, they'd have a much better chance.