On Kim Possible, Dr. Drakken's Dragon Shego is a sort of evil counterpart to Kim. She's a former teen hero herself. The similarities in their overall character design leads some new viewers to think Shego is Kim's Evil Twin.
They also both get together with their partner in crime/justice. There is an episode dedicated to just how similar they are if Shego was good; they are so compatible it ramps up the Ho Yay to very impressive levels for a Disney Cartoon, due to it splitting up the Kim Possible + Ron Stoppable romance.
Though he's considered Kim's archenemy, Dr. Drakken serves as a good counterpoint to Kim's sidekick Ron. Both are not particularly good fighters and leave fighting to their female companions. Drakken is outwardly intelligent, but manages to botch many of his schemes due to incompetence. Ron often acts buffoonish, but it's implied that he holds some innate intelligence. Their similarities are highlighted in the episode "Bad Boy".
Kevin, aka "Kevin 11" from Ben 10. Only a little in his first appearance, but more and more each time he shows up. He starts as a sociopathic kid a little older than Ben with the ability to absorb energy. He absorbs energy from the Omnitrix twice in his debut episode, each time transforming him halfway into one of Ben's alien forms. By the time he resurfaces in his second episode, he's all alien, and can change between them, but can't stay human very long. At the end of that episode, he winds up as a freaky hybrid, incorporating a little bit of human form and aspects of all 10 original aliens, and from then on he's stuck that way.
Gwen also became a Good Counterpart to Charmcaster after stealing her spellbook and using it to learn magic.
In Alien Force, Kevin pulls a Heel-Face Turn and gets his own Evil Counterpart as a result, Mike Morningstar/Darkstar, who also has energy absorption powers. Ben, in the meantime, gets a new Evil Counterpart in Albedo, who doubles as his Evil Twin.
Omniverse has Khyber's alien dog Zed who can transform into monstrous predators with the aid of the Nemetrix, a technology-based example of this trope to Ben's Omnitrix.
Dr. Psychobos, the creator of the Nemetrix, acts as this to Azmuth, convinced that his race, the Cerebrocrustaceans, are intellectually superior to the Galvans.
Negaduck -both versions, the first arguably moreso, as he is the the dark half of Darkwing's personality, given form after he is zapped by Megavolt's Tron Splitter device. He resolves to kill his Posiduck counterpart, so as to conquer the underworld undeterred. The second, from an alternate universe, is no less evil, as he delights in the thought of murder, and at one point tries to destroy all of St. Canard in one fell swoop.
In Metajets, The Stunt-Hawks are a trio of criminals flying newer, more advanced transforming jets designed by the same man who designed the good Metajets.
In Avatar: The Last Airbender, there are numerous parallels between Katara and Azula: roughly the same age, they are both the daughters of leaders with leadership skills of their own, both freakishly powerful and talented prodigies with their elements, both at least occasionally overbearing control freaks and possessed of a dangerous temper when provoked. On opposite lines of the Red Oni, Blue Oni divide they may be, but taking into account their fathers' personalities/influences they are far more alike than one may think.
Azula also serves as an Evil Counterpart to both Zuko and Iroh. As Zuko's, she shows what he could have been if he really did have everything he thinks that he wants (and 50 extra I.Q. points, at least). As Iroh's, she tries to steer Zuko down the wrong path rather than the right one. This is lampshaded in a dream sequence Zuko has, in which he is being consulted by a red dragon and a blue dragon on which path to take in life, good or evil. The red dragon, who advocates good, has Iroh's voice, while the blue, who advocates evil, has Azula's. This situation comes true in Season Two's finale, in which Zuko chooses Azula's way only to regret it.
Zuko has another one in Zhao who is older than him, experienced in war, willing to sacrifice others to further his own career, and seems to have favor within the Fire Nation helping him go through the ranks. It is also shown with the fact that they're also unfriendly rivals in the show always fighting whether physically or over Aang. They also attempt to capture Aang for different reasons, Zuko so he can restore his honor and return home, and Zhao as a vanity project.
Hama serves as another Evil Counterpart to Katara. Both of them went through horrible things during the war against the Fire Nation (Katara lost her mother; Hama was captured and left to rot in a prison cell); however, Hama became so obsessed with revenge that she became no better than those who hurt her, even going as far as imprisoning innocent civilians in a cave simply because they were Fire Nation.
Word of God says they designed Slade to be an evil version of Batman, though Batman himself never appears in the series (except possibly once, in silhouette).
From a team standpoint, the HIVE are the evil counterparts to the Titans, at least before they became Flanderized into joke villains. Brother Blood doesn't start out as an Evil Counterpart to his Arch-Enemy Cyborg, but becomes such during the events of the third season finale.
Vlad to Danny in Danny Phantom. True to the trope, the Not So Different speech is one of Vlad's favourite tactics, leading to the expected denial from Danny.
Captain Planet has an evil counterpart in Captain Pollution, composed of the polluting powers of Super Radiation, Deforestation, Smog, Toxics and Hate.
Zarm is to Gaia.
In Batman: The Animated Series, The Creeper was presented as the Joker's good counterpart, being doused by the Joker's Psycho Serum but turning out as a well-intentioned mad man. Amusingly, he is just as obsessively attracted to Harley Quinn as she is to the Joker.
Roland Daggett is one to Bruce Wayne, an evil man who uses his wealth to achieve ends with very destructive means vs. a responsible billionaire who uses his wealth to improve lives and risks his life to defeat criminals.
In a rare villain to villain example, Grant Walker to Mr. Freeze. As pointed out by a reviewer for the episode Deep Freeze, Mr. Freeze is man who claims to be dead to emotions, but whose emotions - mainly his love for his wife- drive his actions, and what prevent him from carrying out Walker's plan, not to mention hating his frozen state. Walker is a seemingly kind man, who thinks nothing of freezing all but a select few to create his own world, and who prefers the confinement of Mr. Freeze. This made him more of a Mr. Freeze than the original one.
Watch the episodes with Sideshow Bob and you'll realise he and Bart are more alike than either would care to admit. They're both manipulative, clever, and quite self-centred. The difference is that Bart is a nice person deep down and shows genuine remorse for his actions (when they go wrong), whilst Sideshow Bob only cares about accomplishing his goals and eliminates anyone who gets in his way.
Thailog of Gargoyles is an Evil Counterpart to both GoliathandXanatos, ironically enough. He's Goliath's evil clone, but he also embodies the depths of evil of which Xanatos would become capable if he lost the last threads holding him to his humanity. Both characters see Thailog as one of their most dangerous enemies, if not the most.
Lotor's Robeast in Voltron: The Fleet of Doom is an Evil Counterpart to Lion Voltron and Vehicle Voltron.
Dracotron in Voltron: The Third Dimension, which is made up of 5 robot dragons, is an Evil Counterpart of Voltron.
In an episode of The Adventures of Sam and Max, the eponymous duo accidentally release Dangly Deever, a Howdy Doody-style children's show marionette, while futzing with one of the Geek's numerous research projects. This seems harmless enough, until the Geek returns in time for an evil version of Dangly, and several other puppets who didn't get good counterparts, to break free. At the climax, the two Danglies are struggling for dominance while the heroes try to pick out their target.
Men In Black: The Animated Series: The Fmek alien race is the Evil Counterpart to the Arquillian alien race.
The Powerpuff Girls: has two sets. The Rowdyruff Boys are a group of little boys with the same powers but the opposite morality, and were created by Mojo Jojo from snips, snails, and puppy dogs tails. The Powerpunk Girls are from an alternate universe where the evil Oppressor Plutonium (Professor Utonium's own Evil Counterpart) created them to conquer the world. (Mojo Jojo has a Good Counterpart in this reality who is a hero.)
Dick Hardly is one for Professor Utonium, being little more than a sleazy money-grubbing scientist who made knockoffs of the Powerpuff Girls with no legitimate love for them.
The Dreamstone utilizes a non character example, instead one of the title MacGuffin. The Nightmare Stone, much like the Dreamstone is Exactly What It Says on the Tin, a magical gem able to send nightmares to sleeping residents while fending off good dreams. In another reversal, the heroes are made to steal the Nightmare Stone from the villains much like the latter try to steal the Dreamstone throughout the series.
For a character-based example Zordrak may be this to the Dream Maker, an intelligent and highly powerful sorcerer who uses his power to send dreams to the world around him and watches over a population of somewhat loyal bumbling creatures. In contrast to the benevolent Dream Maker however, Zordrak is a Bad Boss vehement on conquest and spreading nightmares.
Scooby-Doo! Mystery Incorporated posits that there was a group of teen mystery busters before Scooby and his crew called Mystery Inc., and their team mascot was a parrot named Professor Pericles. When it was learned that Conquistadors left a treasure in their hometown of Crystal Cove and clues to finding it, Pericles became corrupted and struck a deal with a team member, only to be double-crossed and committed to an asylum. Pericles had since escaped.
The Real Ghostbusters had to deal from time to time with the "People-Busters," their Spirit World counterparts (a similar concept also featured in Tokyopop's Ghost Busted anthology manga). They also dealt with "ecto-clones" of themselves, which manifested when a crack in the Containment Unit bathed their ectoplasmically-saturated original flightsuits in PK energy.
My Little Pony Equestria Girls gives us Sunset Shimmer, a former student of Princess Celestia. Unlike Trixie, Sunset is actually a perfect counterpart to Twilight as Sunset couldn't give two flips about studying, believed herself to be superior, would go so far as to use underhanded tricks to shatter friendships and ruin other people's fun for her own sake. Oh, and turning into a friggin' demon might have a factor in this.
Tooley to Texas in Motorcity. "Threat Level: Texas!" has the two of them interacting for most of the episode('s real time). Kaia is this to Mike, as they both want to stop Kane, but Kaia is willing to harm innocent people in the process. During the Mushroom Samba of "Mayhem Night" Mike sees a literal evil-version of himself, possibly as a reminder of his past working for Kane.
The episode "Jack versus Mad Jack" of Samurai Jack deals with Jack's inner rage building to a peak when he gets bombarded by nearly a dozen bounty hunters. Aku, watching Jack's anger boil, sees that his fury is powerful in its own right and decides to manifest an evil duplicate called Mad Jack to turn it against him. However, Jack soon discovers that Mad Jack's existence is tied to the rage that currently resides in him, so Jack takes a second to cool his head and purge his mind of that rage, which wipes Mad Jack from existence.
Asajj Ventress is this to Anakin. They both used to be slaves on a remote Crapsack World, have been rescued by a Jedi, who were considered somewhat "rogues" by others, both of their rescuers died, and both of them became the apprentices of a Sith Lord. Interesting to note, that while Anakin started slipping closer and closer to the Dark Side in Season 4, she seems to have started to work on a Heel-Face Turn at the end of the same season.
To a lesser extent, Ventress is a counterpart to Ahsoka as well: both of their masters were Jedi who fell to Dark Side, both of them strove to prove themselves worthy of their respective masters, they both started by using a single green-bladed ligthsaber, and picked up Dual Wielding later, and finally the way the Jedi Council abandoned Ahsoka under pressure from the Senate, eerily resembles to how Dooku betrayed Ventress on Sidious's order. They have even come to realize that they have a lot in common.
The Daughter and the Son are respectively the embodiments of the Light, and The Dark Sides of the Force.
Aladdin: The Series gives us Mozenrath to Aladdin. Both of them are very clever and quick-witted, yet they are occasionally prone to letting their youthful impatience and boredom get in their way of completely reaching their fullpotential, and they're both hinted to have rather unpleasant pasts. Oh, and neither of them is ever seen without their faithful animal companions.
Gravity Falls has Gideon to both Dipper and Stan; he has knowledge of the supernatural and a desire to unlock the secrets of the town comparable to Dipper, and he and Stan are both con men while both also having links to the genuine paranormal, but where Stan is a Jerk with a Heart of Gold Gideon is a straight up psychopathic Corrupt Hick.
In one of the weirder cases of this trope, Adventure Time's Marshall Lee is this to Marceline, being a gender swapped Author Avatar of her. He's a much darker and crueler reflection of her, and Marcy almost seems to wish she could be like him. That said, for a Shadow Archetype, Marshall sure seems to hate seeing Fionna cry.
Robot Chicken had a sketch revealing a "Negative Wonder Woman". The most evil thing she does in the sketch involves merely robbing a bank, but she does make herself known to act cruder than the real Wonder Woman. As for costume, since Wonder Woman's leotard leaves her arms and legs exposed, but covers up certain feminine parts, Negative Wonder Woman wears an outfit that covers up her arms and legs, but leaves those feminine parts exposed.
In Dragons: Riders of Berk Hiccup is given one in the form of Egomaniac Hunter and leader of the Berserker tribe Dagur the Deranged. Where Hiccup wants to befriend dragons, Dagur starts out wanting to simply hunt them before deciding he wants to use their power for himself and has his sights set on taking Toothless from Hiccup. Dagur's status as Hiccup's opposite is confirmed in "A View to a Skrill, Part 2" when he forces the captured Skrill to attack Alvin the Treacherous against its will.