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.
In Vampire: The Masquerade, the Sabbat is the evil counterpart of the Camarilla. Or at least, the more evil counterpart (given that all members of both are vampires).
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.
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.
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.