Sun-Tzu Liao is this for Hanse Davion. Both are unparalleled Chessmasters. Both ultimately did what they did to improve the quality of life for their people. And they both frequently use the same methods. Both of them made alliances with neighboring powers that primarily benefited themselves. And so forth. It could be argued that Sun-Tzu is more ruthless, being more willing to sacrifice his own people to achieve those ends, but Hanse Davion has been just as willing to sacrifice his people too. And both of them ended up effectively being deified by their people.
A more accurate example is Victor Steiner-Davion with his sister Katherine. Both were children of Hanse Davion, but raised on different worlds. Victor was very military, and tried to rule through that kind of thinking. Katherine was a political mastermind, gaining power through brinkmanship and guile (and murder). Both considered themselves to be the true heir of Hanse Davion. Neither had any real respect for the other; Victor saw Katherine as a foppish dilettante, while Katherine saw Victor as a manchild playing with wartoys. That they were responsible for the most destructive civil war in Inner Sphere history should not have been a surprise to anyone.
Chuubo's Marvelous Wish-Granting Engine: Billy Sovereign is basically Seizhi, the Best Friend, minus a soul, and is evil enough that he once impaled Leonardo de Montreal on a railroad spike. Seizhi's Arcs in the Glass-Maker's Dragon campaign even encourage the inclusion of a villainous counterpart, referred to as the "Walker in Darkness", in order to fall to your Vice and give you the motivation to reject it.
Elves and Drow elves. Both have a dexterity bonus, a constitution penalty, and bonuses to perception skills, making them adepts at guerrilla tactics (plus, the drow live in the underdark and have darkvision). While the elves are good, drow elves are an Always Chaotic Evil race.
Halflings and goblins. Both are stealthy and athletic, but halflings are known for their courage while goblins are known for their cowardice.
Gnomes and Kobolds: Both are skilled with technical skills (Gnomes are perpetually inventing new things, kobolds are excellent with traps), but gnomes are sturdy and tend chaotic while kobolds are squishy and staunchly Lawful Evil. Their gods, Garl Glittergold and Kurtulmak, are thus evil counterparts to each other as well.
Eberron: the Blood of Vol is basically an evil version of the Undying Court, repackaged for mass consumption. Both involve divine magic without the involvement of Eberron's ambiguously real deities, but the Undying Court seems largely indifferent to the Sovereigns, the Silver Flame and so on, while the Blood of Vol is staunchly Nay Theistic. Both have physical immortality via undeath as a tenet, but the Undying Court use positive energy and become the Undying while the Blood of Vol relies heavily on vampirism and lichdom. Both are led by undead elves, but the Undying Court are a council of Neutral Good deathless elders while Vol is Neutral Evil and is referred to as "the Lich-Queen". Indeed, the most Vol-friendly group of elves of Aerenal, the Stillborn, have adopted a practice of alchemically treating themselves to appear undead, despite being fully alive...that was developed by an Elven lineage that is for the most part staunchly loyal to the Court and who have been doing it for a very long time.
In Werewolf: The Apocalypse, the Black Spiral Dancers are evil counterparts to the Gaia Garou. After falling to the Wyrm, the Black Spirals retained aspects of Garou culture, such as lunar auspices, the Veil, and a Wyrm version of the Litany.
Vampire: The Requiem has Belial's Brood, a sect of Hollywood Satanist vampires who are obsessed with depravation and bringing hell on earth, in contrast with the playable Covenants, who while not exactly nice, are more pragmatic and rational.
Beast: The Primordial then gives us Heroes, who are basically a Knight Templar equivalent Hunters with all their worst traits. Its supplement Conquering Heroes also introduces the Insatiable, who are best-described as just like the Beast, only without a single shred of humanity.
Warhammer gives an interesting example in the (sadly now-defunct) Chaos Dwarfs. They're what happened when Dwarfs get infected with Chaos energy. Abandoning the old Dwarf gods and taking up worship of the bull god Hashut, the Chaos Dwarfs are greedy, tyrannical and merciless, driven by a need to subjugate all before them. They have a real Mesopotamian thing going for them as opposed to the very British/Nordic-flavoured regular Dwarfs.
All over the place in Sentinels of the Multiverse. In particular, this is the point of the Frightful Five, Baron Blade's Villain Team-Up to destroy the Freedom Five. Most of them are Nemeses of the character they're the counterpart for, which means the two deal bonus damage to each other.
Gloomweaver to Nightmist, especially her Dark Watch form. Both are more magical creatures than physical and destroy magical creatures, but Gloomweaver is pretty much pure evil while Nightmist fights for good.
Iron Legacy to, unsurprisingly, Legacy. Evil alternate universe versions are effective like that. While Iron Legacy isn't mechanically a Nemesis, because he is his universe's Legacy, there's still unique dialogue in the digital version between the various Legacies and Iron Legacy.
Inverted with Omnitron-X, who is the Good Counterpart to the original Omnitron.
The Scholar gets two: Biomancer, who is also long-lived and intelligent, but brutal instead of gentle, and Hermetic, another alchemist interested in the Philosopher's Stone, but a poisoner instead of a healer.
Friction (Frightful Five) to Tachyon. Both are speedsters who like to play cards quickly, but Friction is reckless, self-destructive and sloppy, while Tachyon is noted for caution.
Ermine to the Wraith. Both are wealthy people who actually do stuff, but the Wraith is quiet and fights crime for the common good, while Ermine is a notoriously chatty thief.
Apostate to Fanatic. Both are winged and wield a lot of relics, but Apostate is a demonic tempter while Fanatic is radiant and direct. They even have counterpart swords: Fanatic's Absolution and Apostate's Condemnation.
Chokepoint to both Bunker and Unity. Like Bunker, she's got ties to the Ironclad Project, and like Unity, she's a technopath with a need to prove herself. Reinforcing the Unity parallels, her transformation from Choke to Chokepoint involved merging with technology when mortally wounded, the same way that something of Unity survived Iron Legacy's attack in that timeline.
Plague Rat to Chrono-Ranger. Both rely heavily on buffing damage and dishing out tons of it quickly. Plague Rat is the source of the horrible rat monsters that hunt in the Final Wasteland; Chrono-Ranger travels through time killing cryptids to Set Right What Once Went Wrong and prevent the Final Wasteland from existing to begin with.