In the Ultima series, Lord Blackthorne is this to Lord British. The Virtues have evil counterparts as well.
The Guardian ends up usurping the Avatar in his long absence, replacing the doctrine of the Virtues with his own propaganda, the "Fellowship".
In EarthBound, Ness is approached by a time traveler, Buzz Buzz, and learns that he's the hero who saves Earth from an alien invasion. Unbeknown to him (and the player, until the end of the game), Porky — your initial guest character who is totally narcissistic and useless — has been approached by the alien leader, Giygas, to be his right hand man.
Il Lupo (aka The Prowler) in Assassin's Creed: Project Legacy was a fighter trained by the Templars after observing Ezio in action as a countermeasure to the Assassins (specifically Ezio) by equipping him with similar weaponry right down to a hidden blade and teaching him the same skills Ezio knows. Even his attire is similar to an Assassin's. Unfortunately, he was killed before he could ever have a chance to actually face Ezio.
Shay Cormac from "Assassin's Creed: Rogue" is one to Connor from "Assassins Creed III" due to both having very strong morals, and becoming legends for being responsible for The Purge of each other's Orders in the American Colonies/United States, as well as possibly their roles in two of the world's biggest revolutions; the American and French, respectively.
The Mass Effect 2 DLC Lair of the Shadow Broker takes it even further with Tela Vasir, an asari Spectre and agent of the Shadow Broker. She even delivers a Not So Different speech to Shepard, who for all intents and purpose, is working for the equally shady Illusive Man.
Really, the evil counterpart to Shepard in Mass Effect 3 is The Illusive Man. While Shepard is willing to sacrifce himself/herself for the greater good, and reluctantly sacrifices others for the same, TIM forcibly sacrifices others to achieve his goals, to acquire power. While Shepard's sacrifices bring humanity closer to victory, TIM's sacrifces brings humanity closer to destruction.
Achieved in the Multiplayer, with the Phoenix classes, biotic Cerberus defectors, and the Dragoons, which is what would have happened if the Phoenixes had stayed loyal. Same suit? Check. Same attack, different only in color? Check. The Phoenix gets it better, since at least it gets shields.
Also in Multiplayer, the N7 Shadow and Slayer classes are the Good Counterparts to the Phantoms. Skilled in battle ballet? Check. Wicked sword? Check. Invisibility cloak? Hand cannon thing? Check and check, for the Shadow and Slayer respectively.
Bryce Cousland and Loghain Mac Tir, as well. Both are immensely loyal, powerful figures in Ferelden and heroes of the war against Orlais. They are also the only two Teyrns left in Ferelden. In personality and actions, however, they are entirely different, and have diametrically opposed views on the Grey Wardens.
In World of Warcraft you actually get to beat up your own evil counterpart. Or technically, your "inner turmoil" (or for casters, it has often been identified by players as your inner idiot - it only uses melee attacks).
The Warlock class is, lore-wise, the Evil Counterpart to the Mage, as they are usually former mages fallen into the temptation of resorting to demonic energy to make them stronger.
The Lich King's Death Knights, both as a hero unit in Warcraft III and a class in World of Warcraft, serves as an Evil Counterpart to the Paladin (they're even referred to as such) in both games.
Another example is the boss battle Herald Volazj, who actually drives you insane and makes you fight evil twisted versions of your party members. Though, after you beat them, you may help your real party members kill their evil selves.
Shadow Priests are in themselves the evil counterpart to their Light and Holy brethren.
There have been plenty of non-playable evil counterparts to every class, such as the Druids of the Flame for Druids.
Deathwing firmly establishes himself as an evil counterpart to Alexstrasza, being bent on the destruction of life and twisting dragons into genetically-engineered monstrosities.
And potentially Bastila to the player in the first game.
Hanhaar is Mira's evil counterpart.
"Starkiller" from The Force Unleashed has been described as the "photo negative" of Luke Skywalker, and is what Luke may have become had he been trained by Vader instead of Obi-Wan. Starkiller falls more in line with Luke's story after turning to the light, ultimately engaging in a self-sacrificing battle against Vader and the Emperor aboard the half-completed Death Star... For bonus points, in George Lucas's original draft, Luke's original name was "Luke Starkiller."
Many of the Guilds of Lusternia have counterparts in the form of foils, but only the Celestine priesthood have a straight-up Evil Counterpart in the form of the Nihilists: the former are white-winged priests granted angelic companions by extradimensional incarnations of virtues, while the latter are bat-winged priests granted demonic companions by extradimensional incarnations of sins.
A more direct example is Lemon Browning, who is the Alternate Universe version of heroine Excellen Browning. The split came in a shuttle crash. The original Excellen survived without a scratch, while the other died and was rebuilt by her parents into a cyborg.
And Z adds Asakim Dowin to the family of evil counterparts (in this case, of Masaki Andoh), and unfortunately there won't be a white Paladin Shu to stop him.
In the Mega Man games, Bass (AKA Forte in the original Japanese versions). The TV show had Proto Man (Blues in Japan) in this role, despite him being a good guy in the games. This may be because in his first appearance in Mega Man 3, if you didn't know the plot (which, as was common for the time, wasn't actually in the game), it was very easy to mistake him for a villain unless you beat the game. Most likely, though, they just wanted to have a clear cut Evil Counterpart to Mega Man, and Bass hadn't been invented yet.
Zero's own evil counterpart is Ax-Crazy Omega Zero, considering that Omega possesses Zero's original body and uses the same attacks Zero himself uses in Mega Man X. Plus, Omega is what Zero himself would have become if Zero would have been following Wily's plans for him.
Originally, Zero was intended by Dr. Wily as the Evil Counterpart to Mega Man X. However, after his defeat by Sigma (who later ironically becomes the Big Bad of the series), Zero was cured of the virus and became X's Lancer instead.
Both have earlier Evil Counterparts: Mega Man has Quint and Zero has Sigma.
In Mega Man Battle Network, MegaMan no longer has a direct counterpart; Bass is considered one to MegaMan because both are the only Navis who always have distinctive humanity among NetNavis, with Bass being an experiment and MegaMan being's Lan's dead little brother brought back as a Navi, but aside from said trait there is nobody who has similar powers to MegaMan. There is another pairing introduced, though, Baryl and Chaud as well as Colonel and ProtoMan. Both star in 5 depending on the version, and both are leaders who think more logically. Baryl, however, is adopted by Wily and in the 6th game he becomes one of the main villains.
In Breath of Fire IV, Fou-Lu is an Evil Counterpart to Ryu. He's superpowerful. (It's implied by various reactions to them that they are actually also Evil Twins, but the sprites don't actually look that similar, especially since Ryu has short blue hair and Fou-Lu has long silvery hair.)
In the Sonic the Hedgehog franchise, Shadow the Hedgehog was introduced as Sonic's Evil Counterpart. Since then, though, he's become more of an Anti-Hero Counterpart.
Then Shadow got his own evil counterpart in the form of Mephiles the Dark, the main villain from Sonic the Hedgehog (2006) whose form is a copy of Shadow's own shadow.
Sonic's original Evil Counterpart is Metal Sonic.
In a somewhat rare example, the villainous Dr. Eggman has an Evil Counterpart as well, in the form of Eggman Nega. Where Eggman is an Affably EvilAnti-Villain with a sense of morals and heroism, Nega unabashedly loves fear, chaos, and suffering - Essentially, he's what Eggman would be without his human qualities.
Because of the Jungian craziness, Shin Megami Tensei: Persona has this in spades. The main cast of Persona 2 actually have to fight their Shadows, manifestations of their dark sides created by Nyarlathotep. In the original Persona, there's Maki/Mary vs. Pandora and Aki/Maggie, and Kei/Nate vs. Kandori/Guido as businessmen who took different paths.
The tradition continues in Persona 4, where fighting the Shadows of your soon-to-be party members is a major part of the game, generally after the original screams "You're not me!", causing the Shadow to become berserk.
Before they fight their Shadows, the cast of Persona 2 Innocent Sin have to face the Masked Four: leaders of the Masked Circle chosen by the Joker, whether intentionally or only subconsciously, because of their parallels with the main 4 party members. Of the three fought during the game, two of them even wield modified versions of their counterpart's initial personas.
Strega of Persona 3 are the Evil Counterparts to SEES. Specifically, Takaya is the Protagonist's Evil Counterpart, though he's more against your team in general than you specifically.
Adachi of Persona 4 also serves this role for the protagonist. In fact, he even has the same US voice actor and a modified version of the main character's first persona.
Wario was once an evil rival of Mario, complete with evil versions of Mario's powerups. Then he shifted to a greedy Anti-Hero who stole from other villains, soon replacing his dark powerups with the gimmick of Nigh-Invulnerability and bizarre transformations based on how he is injured. On a couple of occasions Wario has actually helped Mario however, both with and without selfish motives.
Later on, Nintendo gave Luigi his own Evil Counterpart in the form of Waluigi.
It's interesting to note that the prefix 'wa, originated from the word "warui" means plenty of things, including "evil" in Japanese. Hence, Wario and Waluigi are, literally, "Bad Mario" and "Bad Luigi". However, their names can also mean, based on the meanings for the word "Warui", " Wrong Mario/Luigi", "Poor Mario/Luigi", "Hateful Mario/Luigi", "Abominable Mario/Luigi", "Wrong Mario/Luigi" or "Inferior Mario/Luigi".
Furthermore, Waluigi´s name in Japanese is an anagram to the word "Ijiwaru". Which means his name has extra meanings such as "Ill-tempered Luigi" or "Sadistic Luigi".
Aside from that, the initial playable characters and their evil counterparts had shared special themes in relation to one another. For example, the series' protagonist Eiji and his evil counterpart Leon had shared a theme of temperament; where Eiji was a hot blooded jerk seeking to get stronger, overtime, he softened up and became more level headed in his pursuits. Leon is a cruel and cocky jerk without any standards, who will do anything in his power to be the strongest and get rid of those who will stand in his way, even if it meant sending them as a sacrifice to Abel's plans. He even desires to challenge Sho to achieve his goal.
In Guild Wars, to progress beyond a certain point in the plot you have to defeat your own character's evil twin in single combat. The doppelganger has the same skills as your character and higher stats, so you can't defeat it by simple brute force; you have to win by outsmarting the AI.
Azel in God Hand has the left God Hand, while the main character, Gene, has the right. It is said that he who possesses a God Hand may be either god or devil; Azel chose the latter route, dubbing himself "the Devil Hand". He wiped out his entire clan (protectors of the God Hands) to test his power, and then sided with the demons plotting to raise Angra.
Final Fantasy IV has Cecil and Golbez. It's revealed that they're blood brothers, and Cecil thinks when he finds out that it could easily be him, that was possessed by Zemus to act as the villain. In the sequel they have mirror movesets, Cecil having White Magic while Golbez has Black Magic, and their Cover and Taunt abilities both draw attacks from allies in different ways.
There is also a clear contrast drawn between Kefka, a Bad Boss who harasses his troops and is generally a menace, to the honorable and beloved General Leo Cristophe.
Final Fantasy VII builds up Sephiroth as Cloud's, but while the link starts as fairly concrete at the start of the game, the reveal that Much of Cloud's backstory was a lie and was, in fact, the tale of his friend Zack pushes this aside.
Spin-offs instead treat Sephiroth as more an Evil Counterpart to Aerith — he thinks he's the last Cetra, she actually is; both had fathers involved in the Jenova Project; Aerith has the White Materia to call Holy, Sephiroth seeks the Black Materia to call Meteor; Aerith is a benevolent protector of the planet, Sephiorth is more in line with an eco-terrorist. Word of God has said they were intended during development to be revealed as siblings, which is why they have similar hairstyles and both have Green Eyes. In a novella set before Advent Children, it's implied Aerith could have created avatars of herself like Sephiroth did, but she felt it more important to let Cloud handle things on his own.
Cloud and Sephiroth's appearances in Kingdom Hearts play this totally straight with them, with Sephiroth sporting a black angel's wing on his right shoulder and Cloud having a black demon's wing on his left shoulder. In the same series, it is even heavily implied, if not outright stated, that the Sephiroth in that game was actually Cloud's Enemy Without, an embodiment of his inner darkness.
In Dirge of Cerberus, all of the Tsviets share something in common with Vincent. Shelke is immortal, Nero wields Darkness, Rosso has similar attire (red clothes, metal gauntlets) and fighting methods, Azul has the same shapeshifting powers, and Weiss is trying to attain the power of Omega, the antithesis to Chaos. Furthermore, he's the vessel for Hojo, who turns into monsters like Vincent, but has no morals or physical prowess to call his own. Oh, they also all use a combination of guns and martial arts, leaning towards guns. Except for Shelke. Rosso and Vincent lampshade this with their discussion on each other's "humanity."
Final Fantasy VIII. Seifer was an evil counterpart to Squall, both using gunblades and been trained at the same Garden. Although Seifer was more ambitious than evil.
Final Fantasy IX had Zidane to Kuja - both created by Garland to lead Gaia to war. Zidane is horrified when he thinks that if things had gone differently, he could be the one doing all the evil Kuja has been doing.
The Final Fantasy X and Final Fantasy X-2 duet has Tidus and Shuyin; one died while failing to protect his beloved, while the other gave his existence and succeeded. They even look alike, and fans speculate the fayth deliberately modeled Tidus after Shuyin in their dream-Zanarkand.
Both Yunalesca and Seymour are evil counterparts to Yuna.
Given his status as Unsent, Seymour was pulling double duty as the counterpart to Yuna and Auron.
Final Fantasy Tactics A2 has Illua, the Big Bad of the game and evil counterpart to Luso. Luso and Illua both have grimoires that have blank pages and are filling up with words as they go on their adventures. If Luso fills out his book, it will give him the power to return home, but if Illua fills out her book, then she gets to summon a great evil demon from another dimension to terrorize Ivalice with. Whether Illua succeeds in defeating Luso or not doesn't matter since once she is slain, her last efforts get recorded in the book and the demon gets summoned anyway.
Kingdom Hearts has Sora and Riku, or Sora and Anti-Sora. Also the Heartless might be Evil Counterparts of either people or Nobodies.
Donald and Goofy have entire races of Heartless counterparts in the first game - the shield-using Defender for Goofy, and the sorcerous Wizard for Donald. On the very rare occasions one drops its weapon (each has a 0.2% chance), the corresponding hero can pick it up and use it immediately.
Looking at the backstory revealed in Birth By Sleep, the case can be made that Xehanort is an Evil Counterpart to Sora. They both grew up at Destiny Islands, they both became Keyblade weilders, they both became a sort of composite being (Xehanort through Grand Theft Me, Sora through absorbing others' hearts), they both became a Heartless and a Nobody. Sora is a Naive Hero and increasingly portrayed as a Messianic Archetype, while Xehanort is a Magnificent Bastard who has recently showed some Fallen Angel symbolism.
Akuma is Ryu'sBlue counterpart in various Street Fighter games and their adaptations. The brother of Ryu's master, Akuma was a student of the same martial art and was also driven by the desire to be the most powerful martial artist, deciding that he was willing to kill those he defeated in the pursuit of true strength, while Ryu ultimately rejects killing. (The exception being in Street Fighter Alpha 2 and 3, where there's an Evil Ryu Secret Character. There, he turns out even worse than Akuma. Whereas Akuma has a sort of moral code, even if it falls heavily under Blue and Orange Morality, Evil Ryu is just a cold-blooded killer who ends up slaughtering the entire cast.)
Ultra Street Fighter IV gives us Decapre for Cammy. Aside from being the her twin, the former also represents what the latter could have become had she not broken free from her brainwashing.
Liquid Snake from Metal Gear Solid is one of the few literal examples. He and his twin Solid Snake were cloned from the same man, and although Liquid was (supposedly) genetically superior than his brother Solid, Liquid grew up believing the opposite and wanted to kill his father Big Boss to prove his worth. When Solid takes away that chance from him by defeating Big Boss first, Liquid decided to take his aggression to Solid instead.
Big Boss himself counts.
Claudia of Silent Hill 3 was raised in the same nightmarish cult as Alessa Heather by a similarly abusive parent and may also possess the ability to summon the series' iconic Dark World, however she embraced the cult's teachings and their plans of resurrecting "God" while Alessa Heather rejected them.
Vasteel Original in Thunder Force V is prototype of player's Vasteel fighter. Also Vasteel Nocht from Thunder Force VI which is large fighter that utilise weapon similar to player fighter from previous three games.
The gnomes introduced in Overlord II are a good counterpart to your minions. Unfortunately for them, in the setting, "Good" means either "self-serving Jerk Ass using their supposed virtue as free license to do whatever they want" or "obnoxious, ineffectual idiot", and they got stuck with the latter version.
Still, another example of a Good Counterpart for the Evil OverlordVillain Protagonist would be Queen Fay, leader of the Elves and the reigning being of Light Magic (you being Dark Magic). She still ends up coming to you for an Enemy Mine against the Anti-Magic Empire in which she ends up sacrificing her energy to power the Overlord's Tower Heart, ending with her corruption and becoming a Fallen Hero.
Alex Mercer from Prototype has to contend with Blackwatch Super Soldiers who have controlled exposure to the same virus powering him It IS him, but that you won't find out for a while, as well as the Hunters who have similar powers - all the way up to the Supreme Hunter also being able to shapeshift - but are clearly inhuman. It's not so much Good Counterpart versus Evil Counterpart as it is Evil Versus Evil though.
From Morrowind, there's the Thieves Guild, which is definitely shady, but has elements of Gentleman Thief and Just Like Robin Hood, and the Cammona Tong, a xenophobic Dunmer nationalist crime syndicate that despises the Empire and has absolutely no code of honor.
Also from Morrowind, there's the Morag Tong, an underhanded, though noble assassin’s guild, and the Dark Brotherhood, an organization of murderous scumbags who will kill anyone if the price is right, or just to appease their "god".
Necromancers in Tamriel have always been portrayed in a "dark grey" light. The Order of the Black Worm from Oblivion, however, show just how evil and depraved they can be if they want to. It doesn't help that the Order's leader is an Omnicidal Maniac.
The Dragonborn expansion to Skyrim reveals that the Dragonborn has one in the First Dragonborn, an undead Dragon-Priest who once ruled over Solstheim and now seeks to return to life.
Also in Skyrim, the Thieves Guild have somewhat become this to the Dark Brotherhood, maintaining their traditional mutually beneficial working relationship and sharing information on prospective jobs with each other, with the understanding that they'll not try to kill people during robberies, if the Dark Brotherhood don't rob people during assassinations.
Neverwinter Nights 2: Ammon Jerro, who, like the player character is collecting the shards of the Silver Sword of Gith to reconstruct it, aims to vanquish the King of Shadows, and has collected a group of (involuntary) allies to aid him. Possibly subverted in that the player can be just as evil as either character - or potentially more so.
The Mask of the Betrayer expansion has Arraman, who isn't really 'evil' as such but opposes your character at every turn, unless you give up on the Crusade.
Neverwinter Nights has Maugrim for Aribeth (for a while), Haedraline for Drogan in Shadows of Undrentide, and Sabal for Nathyrra and the Valsharess for the Seer in Hordes of the Underdark.
Various community expansions have examples. Alex / Mordred for the player in the The Bastard Of Kosigan and Vico for Bran (and in part Anden, though his role is more of a Foil to Vico) and Arto Benthur (something like that) for the player in A Dance with Rogues are probably the best, though those modules are also the ones with the best reoccurring characters.
There are a couple present in the Soul Series. The most direct example is Lizardman to Sophitia; both are Greek warriors chosen by Hephaestus, but while Sophitia succeeded (sort of) in her mission and returned home, Aeon Calcos failed, was transformed into a horrible lizard monster and swore revenge on the god that had abandoned him.
Astaroth and Rock share this dynamic, because Astaroth is an Evil Knockoff of Rock.
The RPG, Sailor Moon: Another Story has a set of evil counter parts for Moon and the Inner Senshi known as the Opposito Senshi. Each is named for a Babylonian god or goddess that is roughly equivalent to the powers and role of the Sailor Senshi. Moon has Sin, named for the Moon god. Mercury has Nabu, named for the god of wisdom. Venus has Ishtar, named for the fertility goddess. Jupiter has Marduk, named for king of the gods, and Mars has Nergal, named for the fire god. The Ayakashi sisters mentioned above also make a short appearance.
The Baldur's Gate series firmly positions Sarevok as this to the PC. In the first game he's the only other Bhaalspawn you (knowingly) encounter, but even in Throne of Bhaal where CHARNAME's evil siblings are ten a penny, he's still firmly positioned as the example of what CHARNAME could have been.
Inverted somewhat in the Dungeon Keeper series as most of your minions are evil counterparts to the forces of good, with the biggest example being Black Knight and Knight. Other examples include Warlock/Wizard, Dark Elf/Elf and Vampire/Monk.
In Millennia: Altered Destinies, McDonald's Evil Counterpart is an alternate timeline version of McDonald who was recruited by the Microids instead of the Hoods. The other McDonald flies an identical XTM but uses the ship to undermine the player's actions. Unlike the other examples, there is no way to get rid of the other McDonald.
City of Heroes: Going Rogue has this in spades. In the Mirror Universe of Praetoria; players will encounter familiar names and faces, sometimes in the most unlikely places. But due to the game's fluid alignment system, they can be your allies, or your enemies. Among them are:
Emperor Cole, counterpart to Statesman, single-handedly saved the world in the Hamidon Wars and now rules the world with a gold-plated, iron fist.
Praetor White (aka Marauder), counterpart to Back Alley Brawler, runs Praetoria's Powers Division.
Praetor Tilman (aka Mother Mayham), counterpart to Sister Psyche, is in charge of the Seers, Praetoria's Thought Police.
Praetor Sinclair (aka Chimera), counterpart to Manticore, is Emperor Cole's personal assassin.
Praetor Berry (aka Neuron), counterpart to Synapse, has made hundreds of scientific advances singlehandedly.
Metronome, counterpart to the Clockwork King, behaves much like his Primal Earth counterpart, including his obsession with Penelope Yin.
Penelope Yin, counterpart to herself, is a Resistance spy in Mother Mayham's mental hospital.
Malefor from The Legend of Spyro trilogy seems to be this to Spyro. Both are Purple Dragons, both were, according to Chief Prowlus and the statues of him all over the place, heroic in their youth, and both were trained freely by their elders in the Dragon Elements. The difference is Malefor let his power go to his head and went mad with power while Spyro remained good hearted (though Spyro was raised by dragonflies which may have had something to do with it). Malefor is aware of this and worked it into his Not So DifferentHannibal Lecture.
In Hitman: Blood Money, Mark Parchezzi III is this to Agent 47. Even though 47 can be viewed as a villain, he is shown to have a set of values and morality, while what little is seen of Parchezzi shows him to be completely without scruples. Plus, while 47 performs rather indiscriminate hits, Parchezzi works for the Franchise, a clandestine government group with the goal of keeping human cloning illegal so that nobody else may benefit from it.
DarkLink. In some games, Dark Link is just a mid level boss and in other games, he's a full fledged villain. Dark Link uses a sword and shield in exactly the same way as Link and frequently mirrors Link's attacks to block them. However, Dark Link never uses items besides the sword and shield.
Also, The Legend of Zelda: Skyward Sword's Ghirahim as Demise's sword to Fi as Link's sword. His persona was carefully crafted to be Fi's polar opposite. Fi is fairly emotionless and speaks in percentages. Ghirahim is flamboyant to the extreme, and very open and dramatic. Once his true form is revealed, his text boxes look similar to Fi's, albeit black. Demise's weapon even looks like a dark version of the Master Sword- even down to an upside-down Triforce on the blade.
Meta Knight from the Kirby series has Galacta Knight. Both have very similar appearance, attacks, and movesets. The primary differences between the two are that Galacta Knight lacks Meta Knight's sense of chivalry, and Galacta has a more angelic appearance compared to Meta Knight (White feathered wings and brighter colors compared to Meta's bat wings and dark colors).
Crash Bandicoot has the obviously titled Evil/Nega Crash, his alternate universe equivelant from the Tenth Dimention. Fake Crash (a goofy lookalike created from "an experiment gone horribly wrong") interchanges between being an antagonist or occasional friend of Crash, similar to Wario.
Crash Bash plays this straight, having two teams (good versus evil). Former villains Tiny and Dingodile become part of the good team, with Koala Kong and Rilla Roo representing their counterparts for the evil team.
Mutons of the new X-COM: Enemy Unknown have been described like this, an alien SEAL Team Six to fight your own troops.
In Alpha Protocol, Conrad Marburg is something of an evil counterpart to Mike; a rogue agent from a previous incarnation of Alpha Protocol called Deus Vult, who like Mike was cut loose and falsely declared rogue because it was politically convenient. Unlike Mike, who's still trying to get to the bottom of the conspiracy, Marburg lost faith in the government and now works for Leland.
The SA-X from Metroid Fusion is stated by Samus herself to be the embodiment of her potential for evil. It has all of her EXACT abilities, but no heart or conscience.
Dark Samus from the Metroid Prime trilogy also fills the role of evil counterpart to Samus. Dark Samus has abilities quite similar to Samus' abilities, though her moves are a slight variant of Samus' moves plus she has her own abilities as well. The games' scan logs state that Dark Samus is quite intelligent and can manipulate other races to benefit her own agenda, which is to spread the corruptible Phazon across the galaxy.
Several classes in Everquest II have good and evil counterparts. The Paladin, Swashbuckler, Conjurer, and Mystic, have evil counterparts in the Shadowknight, Brigand, Necromancer, and Defiler, respectively. Previously, the Monk, Ranger, Illusionist, and Templar had evil counterparts in the Bruiser, Assassin, Coercer, and Inquisitor, respectively, but these eight classes are now neutral (taking the number of neutral classes to seventeen).
Tales of the Abyss elevates this to an art form. Every single member of the party has an evil counterpart in the Six God-Generals, and the Big Bad, Dorian General Van Grants, is pretty much an Evil Counterpart to half the party:
Luke's evil counterpart is Asch, as he's Asch's clone
Tear's evil counterpart is Legretta, who trained her to fight.
Anise's evil counterpart is Arietta, who was a Fon Master Guardian before Anise took over her job.
Natalia's evil counterpart is Largo, who seems to have her sense of honour and dedication, and is also her father.
Jade's evil counterpart is Dist, who grew up with Jade and idolized him; they created fomicry together. Well, more like Jade created fomicry and Dist was there when it happened.
Guy's evil counterpart is Sync; or at least, the game would have you believe that. This is a Red Herring - Sync is counterpart to Guy in terms of their Lightning Bruiser fighting style, but story-wise, he's another clone of the original Fon Master Ion, making the current Ion his Good Counterpart.
Big Bad Van is personally connected or mirrored by about half the main party. Luke is his student and the product of his fomicry experiments, and both are primarily seeking a way to avert the Score. Guy is, like Van, a survivor of the sinking of Hod; initially, they both want revenge for their painful childhoods, but Guy manages to overcome his bitterness while Van takes it...wayyyy too far. Tear is Van's sister, obviously. Jade is also a practitioner of fomicry, but while even he realizes fomicry is amoral, Van sees it as the way to recreate the world and save it from the Score.
Messiah: In the final boss fight, Bob the cherub meets Satan's imps, who too can possess people and who look like babies, though demonic ones.
In Um Jammer Lammy, Lammy has Rammy, although it's something of a parody as Rammy has no real relationship with Lammy at all, and Lammy seems to have very little idea who Rammy even is. Rammy can also be quite helpful in certain game modes.
The Noodle Captain and Parappa in Parappa The Rapper 2 - both are obsessed with avoiding a certain food that has become boring, both have eccentric scientist fathers and missing mothers, both use rap to deal with things.
In the early Tekken games (more so the first one), there would be 8-10 default characters, and consequently 8-10 sub boss characters, specifically designed to match up with their corresponding default character and vise versa, as a 'rival' (i.e. one would always fight the other on Round 8). Most of these were actual counterparts of the default character, and in the first game they were literally clone characters too. Examples would be what Anna is to Nina, as well as what Armor King is to King, or what Kunimitsu is to Yoshimitsu. Their Evil Counter part nature was due to most of their intentions and/or employers. i.e. Nina was sent as an assassin to take down the Big Bad where as Anna was working for them. Or King wanting to use the tournament winnings to fund an orphanage, where as Armor King didn't care about King's orphanage and just wanted to prove he was better (as well as being generally quite a dark and mysterious character). Yoshimitsu was the leader of a clan who wanted to steal from the rich to give to the poor, but Kunimitsu wanted to steal from the poor to give to herself (and even stole from her own clan). Later Tekkens kept all these characters, but from Tekken 3 they scrapped the sub-boss system associated with it.
In Robopon, Sun-Zero is this to Sunny, and Negapon is this to Gigapon.
In the XCOM: Enemy Unknown expansion Enemy Within, an evil organization called EXALT is revealed to be secretly in league with the aliens, although they have their own mysterious goals. Their operatives use the same tactics as your own XCOM soldiers, and their weapons are identical in stats (but less boxy) to your own firearms and laser weapons (EXALT never develops plasma). Like your soldiers, EXALT uses Meld to enhance their operatives, although they never build MEC Troopers. Even their HQ's location is opposite to yours. The XCOM base is deep underground, while the EXALT HQ is on top of a skyscraper. When storming it, your soldiers find a hologlobe identical to yours but red in color, although their HQ is more aesthetic than functional in stark contrast to the XCOM base.
Yggdrasil aka Mithos the Hero in Tales of Symphonia could be considered as such to Lloyd, both of them starting out as well-intentioned Determinators, though while Lloyd eventually learns when to back down and think things through, Mithos remains stubborn and unwavering to the bitter end, which causes his Start of Darkness (his last words even have him calling Lloyd "my shadow" and proclaiming that he "stands at the end of the path I chose not to follow.") He also has a lot in common with Genis, both being disillusioned half-elves and having to suffer the persecution that comes from being such, though Genis eventually learns to accept the humans who persecuted him, while Mithos continues to be bitter and resentful towards them.
In Star Trek Online, your character doesn't get an Evil Counterpart via Mirror Universe, but the ships do. And these ships are also playable via lockbox drops.
First Encounter Assault Recon2: Project Origin, Sergeant Harold Keegan eventually becomes this to the Player Character Michael Beckett. He's a member of Dark Signal like Beckett, and matches or possibly even surpasses Beckett in terms of psychic potential, but has questionable mental stability. After Alma possesses and Mind Rapes him, he learns that Beckett is (completely unwillingly) Alma's favourite, and becomes a Crazy Jealous Guy obsessed with killing Beckett, and capable of using Beckett's Bullet Time powers.