However, Link is a Legacy Character, and no version of him has fought Ganondorf more than once. It is possible that Ganondorf considers all pointy-eared, green-suited blond boys to be his Arch Enemy, while each Link just thinks of Ganondorf as another Rogue.
However each Link is usually educated about the Triforce and how they are fated to face Ganon some way or another. But particularly Link from The Legend of Zelda: The Wind Waker had a grudge against Ganon for kidnapping his sister and Zelda and Link from The Legend of Zelda: Ocarina of Time was the first Link to face Ganondorf for endangering Zelda, killing the Deku Tree, and directly ruining every other society he had to rescue.
Justified, and borderline Deconstructed, in The Legend of Zelda: Skyward Sword. Ganondorf is the reincarnation of Demon King Demise's endless hatred for Link and Zelda, and that continues to haunt them even as they keep reincarnating. The three are bound to fight for eternity.
It's also mildly subversive, since the revelation that Zelda is the mortal incarnation of Hylia, the goddess who initially sealed Demise, means she was his original Arch Enemy, not Link.
Dr. Ivo "Eggman" Robotnik is Sonic the Hedgehog's Arch Enemy. The same goes with MetalSonic who was programmed by Eggman for the sole purpose to destroy Sonic.
This, like every other trope, gets lampooned in Kingdom of Loathing: the player receives a quest from their guild to retrieve an item stolen by their Nemesis. The player wasn't aware that they even had a Nemesis before that.
Ridley in the Metroid games, to Samus Aran. This one is personal, since Ridley trashed Samus' home of K-2L and personally killed both of her parents. Ironically, the Metroid manga (which was made by Nintendo) has a brief scene where a 4-year old Samus, not yet knowing what Ridley has done, tries to make friends with the giant space dragon.
When Samus approaches him, Ridley is watching the chaos and fire his pirates have caused, and actually gets a sad look for a moment when he sees her. Then Samus' mother runs to save her from Ridley, and he promptly goes back to normal and kills Samus' mother in front of her.
In the manga, he also mocks her about how he killed her parents.
The original Street Fighter had Sagat as Ryu's original Rival, and it may have been that way ever since.
Fatal Fury has Geese Howard, who could practically be considered an Arch Enemy to Southtown as a whole. Terry Bogard actually winds up adopting his son, Rock (who despises his father anyway, since Geese abandoned Rock's mother).
Iori Yagami and Kyo Kusanagi in The King of Fighters. Iori really does seem to have no life outside of messing with Kyo. After the events of KOF XI, they both get a mutual Arch Enemy in Ash Crimson (who, like Bison before him, has that special talent for pissing off near anybody he comes into contact with).
Dracula has the Belmont clan (as well as the Belnades and Morris families) as his running archenemies in the Castlevania games.[[note]] The Belmonts have to destroy Dracula. They are fated to do so. Dracula makes it easy by actively pissing off the current Belmont. The Morris family, however, has no such problem with Dracula, instead being chosen by the Belmont clan to defeat the vampire out of necessity when they can't. It's a confused mish-mash, but the end result is that Dracula has the Belmont clan as his arch-enemies, but it's one-way and he should really stop exacerbating the situation.
According to the prequel Lament of Innocence, Dracula's real Arch Enemy is Sara Trantoul, whose soul empowers the Vampire Killer.
Mortal Kombat has these all over the board. Liu Kang's Arch Enemy is Shang Tsung, Sonya Blade has an Arch Enemy in Kano, Scorpion has Sub-Zero and Quan Chi as successive archenemies, Kitana has her evil clone Mileena, Jade has Tanya, Raiden has Quan Chi and Shinnok as archenemies, Kung Lao has a nemesis in Baraka, Jax has his in Hsu Hao, Cyrax has his Evil Counterpart Sektor and everyone from Earth Realm had Shao Kahn as a nemesis.
In the Metal Gear Solid series the main protagonist is constantly facing of against Ocelot and/or Liquid, though none of them'd ever use titles as arch-nemesis.
The end of the world be damned, nothing will stop GDI and Nod from attempting to destroy the other, an alien invasion bent on killing everyone is only grounds for a short ceasefire, which doesn't even last halfway through the invasion.
The Protoss are archenemies of the Zerg, primarily because the Zerg had driven them from their homeworld of Aiur.
The Protoss themselves are divided. The templars are frequently at odds with the Dark Templar. However, because of the Zerg, the two factions are being forced to cooperate and may actually begin to respect one another.
Jim Raynor considers himself an arch-enemy of Arcturus Mengsk, although Kerrigan also considers herself this.
Varian Wrynn is technically the Arch Enemy of Thrall, though this is mostly one-sided since it's only really Varian who wants to kill Thrall, while Thrall himself would gladly declare peace. Meanwhile, Garrosh Hellscream represents the anti-Alliance hate on the Horde side. He and Varian almost try to kill each other on a diplomatic meeting.
Almost is being generous, they were trying to kill eachother, someone else just got in the way.
Kl'jaeden and their subservient eredar are definite arch-enemies of the whole draenei race and their leader Velen - they once were one race, before Sargeras arrived with The Corruption. From then on, draenei where on the run from eredar for millenia, until they settled on Azeroth for their final stand.
The Arch Enemy concept is also presented with Outland factions. Major bad guys there are represented by two races - blood elves under the rule of Kael'thas Sunstrider and various demons, partly led by Illidan. Major player friendly fractions, Aldor and Scryers, don't get along very well and have different opinions - Aldor chose demons as their Arch Enemy, while Scryers prioritize stopping Kael'thas' elves.
In a lesser example there is Loken, Arch Enemy of Thorim, who orchestrated first his Heroic BSOD, then the recovery from it, which only led into another trap.
Deathwing, leader of the Black Dragonflight, is the Arch Enemy of Alexstrasza and the other surviving Dragon Aspects.
Twilight's Hammer has been the arch enemy of the Earthen Ring, a shamanistic organization dedicated to preserving & protecting the elemental balance of Azeroth and Outland, since before Cataclysm.
Daiku no Gensan - The President of Kuromoku-gumi, Hyosuke Kuromoku, for Genzo. Only one game in the series has not featured the Kuromoku-Gumi and Hyosuke as major villains.
Crash Bandicoot - Crash has Doctor Neo Cortex. In the same series there is also the rivalry between sentient voodooo masks Aku Aku and Uka Uka
Asha the Assassin becomes Iji's Arch Enemy after losing their first fight. Originally, he was only after the bounty on her head (and the fame).
Empire Earth's 2nd campaign focuses on Great Britain and France's feud through the ages.
Fate/stay night - Shirou gets two, depending on which route you're in. His possible future self Archer is the antithesis of his ideals, yet embodies them. The two are completely incompatible. And allies, at first. The other is Kotomine, who understands Shirou better than anyone else in the Visual Novel. He's also the first person Kotomine met who was like him, a person without a real sense of self. They get along rather well in their own way, they just happen to be completely and utterly opposed to one another.
In God of War, Kratos' Arch Enemy is Zeus. No other enemy, even Ares, commands as much of Kratos' time and energy as the King of the Gods. They are truly arch enemies when you consider that Zeus wants to kill Kratos to restore order to the world, and Kratos is willing to destroy Zeus and Olympus in order to get his revenge.
In Final Fantasy VII, it's actually pretty one-sided; the protagonist, Cloud, eventually has plenty of reason to hate the Big Bad, Sephiroth, but Sephiroth barely acknowledges Cloud at all, and as an insigficant pawn, until the very end when Cloud's group actually beats him. After this, as in the movie Advent Children (or Dissidia, below), they certainly are arch-enemies both ways, though it's possible the very reason Sephiroth has it in for Cloud is that he hates having been beaten by someone so insignificant.
The prequel Dissidia 012 reveals the Emperor is actually more an Arch Enemy to the Final Fantasy X cast as an Expy of Seymour — he manipulates Tidus and Jecht into fighting for the sake of his schemes and isn't pleased when Yuna tries to get the two to work out their differences peacefully. In a less direct example Exdeath is the enemy of the Final Fantasy IV cast, being Kain's designated rival and his death in that cycle being caused by Golbez disrupting his control over the Manikins so Kain can get past them and challenge Exdeath. Also puts a new spin on the scene of Exdeath accusing Golbez of treachery and Cecil protecting him.
Ultimately, Sora and Xehanort in the Kingdom Hearts series. Sora is the All-Loving Hero, while all the conflict in the games was caused by Xehanort in one way or another.
However, Maleficent also serves as this to Sora, as she constantly antagonizes him during his journey.
Riku's arch-enemy is Xehanort's Heartless/Ansem, the Seeker of Darkness. He represents every bad decision Riku made in the first game, stole Riku's body at the end of those bad decisions, and spent a lot of time as Riku's Enemy Within. Not even being purged from Riku's heart is quite enough, as they end up fighting each other all over again in 3D.
Legacy of Kain gives us Malek and Vorador in Blood Omen, The Sarafan Lord and JanosAudron in Blood Omen 2, and Kain and Raziel throughout the series. All of these are slightly one sided, though. While Malek had a deep personal hatred for Vorador, Vorador didn't think much of him and for the most part hated his order and humanity in general. Janos hated the Sarafan Lord for holding him prisoner for four hundred years, starving him of blood but the Sarafan Lord's issue was with vampires in general and he considered Janos little more than a tool. Raziel, likewise, hated Kain on a very personal level, but Kain's actions against him were necessary evils. Kain himself had much more personal grudges against Malek and the Sarafan Lord than he did against Raziel, and possibly his true arch enemy was Moebius. And in the end it turns out Kain was the arch enemy of the Elder God, who manipulated people across centuries to try and kill Kain, due to Kain's destiny to become the Scion of Balance, the only being that can destroy the Elder God.
In the second game The Exile has three: each of the Sith Lords which reflect an aspect of herself. The most prominent is Darth Traya whose fate is bound up with the Exile whether they like it or not.
Space Quest: Sludge Vohaul, despite appearing in only two games (but heavily implied to be behind the events of the first).
King's Quest: The Black Cloak Society to the Daventry royal family. The extent of which of the series' foes were part of the Society is debatable, but at least four (Hagatha, Mannanan, Mordak, Alhazred) have some kind of tie. The Fan Remake of King's Quest II cranks it up a bit with a designated Arch Enemy, Morgelien (aka "The Father").
While Ragna is dedicated to ending the Big Bad Terumi's existence, he believes that his true Arch Enemy will be his brother Jin once his "Power of Order" awakens since Ragna may be the "Destroyer of the World" that the "Power of Order" is meant to fight.
Terumi is an Arch Enemy to the remaining Six Heroes, Kokonoe, and Rachel since his betrayal of them was far more personal (murdered Jubei's wife/Kokonoe's mother Nine, sealed Haku-men in the Boundary, insults the master to whom Valkenhyn holds Undying Loyalty, and has been dueling Rachel in a battle of wits over thousands of years worth of time loops).
Carl's greatest foe as of Continuum Shift is his father Relius, who added his own daughter (Carl's sister) Ada's body and soul to the Nox Nyctores Nirvana and used the information he gleaned from that experiment to create a superior puppet — using Carl's mother Ignis.
Bang used to consider Jin to be his Arch Enemy, but thanks to Character Development has moved passed this. He now considers the system behind the NOL itself that ordered the attack on Ikaruga to be his Arch Enemy.
Even Taokaka has one. She and Arakune frequently come to blows since he terrorizes the Kaka clan village and she is its protector.
Tsubaki becomes her former best friend Noel's Arch Enemy thanks to Terumi's influence, the trauma of losing her sight to Izayoi, and her deep-rooted jealousy of Noel over her being chosen to be by Jin's side.
Relius Clover has a secondary enemy in Valkenhayn, as the two have a long-standing rivalry prior to the Dark War; this was suspended when Relius fell into the Cauldron the day the Black Beast emerged, but has reawakened with Relius' re-emergence.
The Grey Wardens and the Darkspawn of Dragon Age: Origins. The Grey Wardens were founded specifically to prevent the Darkspawn from destroying Thedas and will do anything to accomplish this task. The feeling is mutual during Blights — Archdemons will go out of their way to kill the Grey Wardens once they can sense their location since they know that only Wardens can permanently destroy them.
Each respective origin (except the Mage and Dalish) end with the Warden gaining one of these. Arl Rendon Howe for the Human Noble, Prince Bhelen for the Dwarf Noble, Jarvia for the Dwarf Commoner and Vaughn for the City Elf.
Teyrn Loghain serves as this for Alistair. Loghain earned Alistair's hatred for his desertion at the Battle of Ostagar, leaving the King and the Grey Wardens to die. Loghain meanwhile fears the threat that Alistair poses to his Regency, since as bastard son of King Maric, Alistair is the closest legitimate heir to the throne.
Shale considers Birds to be her personal nemesis, having endured thirty years of being covered by their droppings whilst frozen as a statue in Honnleath. Indeed, one of the first thing she does after being reawakened by the Warden is to stomp on a chicken and according to Dragon Age II, the pigeon population of Ferelden has mysteriously dwindled since the end of the Blight.
In the sequel, Dragon Age II, some of Hawke's companions have archenemies. Danarius for Fenris, Bartrand for Varric, and Castillon for Isabela. Meredith and Orsino are also mutual archenemies. Anders becomes one for Sebastian after the former destroys the Chantry.
Commander Shepard has a lot of powerful enemies: Saren Arterius in the first game, The Illusive Man and Kai Leng in the third game. However, Shepard's archenemies are the Reapers, and (s)he is theirs. They consider Shepard to be the greatest threat they have ever faced, and Shepard is the only thing in existence that has ever made the Reapers feel fear.
The God Wars Dungeon in Runescape would imply that the four Gods involved consider each other Arch Enemies, since even after thousands of years, the 4-way free-for-all is still going on. Saradomin and Zamorak, even though they aren't technically the "Good" and "Evil" Gods.
In Ace Attorney, Phoenix Wright has Miles Edgeworth for most of the first game, although their relationship becomes exponentially more friendly after Wright defends Edgeworth.
Marv claims to be this in Custom Robo Arena, but in practice he's just an idiot who won't leave you alone.
Touhou: Mokou vs. Kaguya. Good thing for them: killing each others over and over and over again is how they kill their (potentially infinite) time. Figuring out how to kill each others in new and interesting way is their joy in life, and sometimes they let other people in on their exquisite "pleasure".
UNSC and Covenant in Halo, specially the Spartans and the Elites (though the latter take the rivalry much more personally). They've been fighting for decades, with humanity trying to stave off extinction at the hands of the Covenant. But later, it's revealed that humanity as a whole has a far more deadlier archrivalry with the Flood, a highly virulent and intelligent parasite dating back to the time of the Forerunners.
The Forerunner Saga and Halo 4 reveal that the Forerunners themselves were this to a highly-advanced prehistoric humanity, with the modern form of the rivalry represented in the conflict between the Master Chief vs. the Ur-Didact.
The Final Fight series has the Mad Gear gang as collective arch-enemies for Mike Haggar and his allies, since the first iteration of the gang (then led by Belger) kidnapped Haggar's daughter Jessica in the first game, and their second incarnation in the second game kidnapped Guy's fiancee and master as revenge (though since Guy's not around, said fiancee's sister Maki steps in instead). In the third game, the Skull Cross gang are arch-enemies for Dean since they killed his family, and in Streetwise Father Bella is this for both Kyle and Cody since he's actually the brother of the slain Belger who had changed his name to hide his true identity.
In the Streets of Rage series, The Syndicate leader Mr. X is the arch-enemy of the protagonists, specifically in the second game where he kidnaps Skate's brother Adam for contributing to his defeat in the first game, and in the third game where he was instrumental in Zan's transformation into a cyborg.
In the fan-made remake of the game, Shiva is arguably this to Axel, as well as being The Rival. The whole Syndicate is this for Rudra, since they kidnapped her sister to force her servitude.