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Miho in Megatokyo seems to fashion herself as an Evil Counterpart to Yuki. She has the same powers, and when she awakens Yuki to her powers, says that Yuki's are based on love, while hers are lonely and dark. But then again, no one ever knows what's with Miho.
Karnak (now the recently deposed King of Hell) and Dominic's father Donovan. Both were orphans raised in foreign lands by a different race/species (orcs raised Karnak and elves raised Donovan). When the two of them met they even became friends, though Karnak never did appreciate Donovan's sense of humor. Unfortunately, they both fell in love with the same woman, but Miranda only loved Karnak as a friend and had already given her heart to Donovan. This frustrated Karnak so much that he grew to despise Donvan and invoked a brutal tradition of orc culture and tried to kill Donovan and take Miranda for himself.
The Order of the Stick has the Linear Guild, a team of Evil Counterparts to the titular band, led by Elan's Evil Twin Nale. After their first defeat, Nale recruited replacements to purposefully continue the "evil opposites" theme.
Taken to its logical conclusion with Yokyok, who is actually a GOOD counterpart to the Chaotic Evil Belkar Bitterleaf.
Belkar is interesting example in that so far he had four evil counterparts, two of which (Yekyek and Yukyuk) were pretty much like him and two of which were his opposites - good Yokyok and Lawful Kilkil.
Crystal to Haley.
Redcloak seems like he is Hinjo's evil counterpart.
Roy however insists that Thog is not his Evil Counterpart and is merely just different from him, stating that there has to be more to it than just Roy being a Genius Bruiser and Thog being Dumb Muscle.
Later on however, Thog is replaced by General Tarquin, a highly intelligent Fighter. He even states that he's joining in partly because he sees Roy as a Worthy Opponent.
From Empire of Blood we have General Tarquin, who is evil counterpart to both Roy (being intelligent fighter and competent leader) and Elan (as they share their love for storytelling and drama) and Lord Shojo, as they both rule their kingdoms through deception of being powerless, Shojo by faking being senile and Tarquin by pretending to be The Dragon to easily-manipulated Empress of Blood. There is also Durkon's evil counterpart Malack. Later on, we meet two other members of Tarquin's former adventuring party: Laurin Shattersmith, whose Hair-Trigger Temper and fondness for blasting things with powers make her quite similar to V with a touch of Fantastic Racism, and Miron Shewdanker, whose blunt sarcasm, penchant for nicknames and method of dealing with problems makes him a human, magic-wielding version of Belkar.
In Sluggy Freelance Kusari serves as the Evil Counterpart to Oasis. They're both superbly skilled, (seemingly) immortal assassins created/raised by Hereti Corp, and Kusari even claims they're sisters. Since Kusari has never been seen without her mask on, speculation rages as to whether or not she is actually an Evil Twin.
Lord Tedd in El Goonish Shive along with Shade Tail. Ellen tried to be this for a while but quickly gave up on it.
In 8-Bit Theater with the main characters being the Evil Counterparts of the true Light Warriors which travel the world since then stumbling from one disaster into another. Also, there are the other warriors which are also (mostly) way less evil than the protagonists.
Shortpacked! gives us McAwesome's Parasailing and Chocolate Bakery... or, more accurately, the titular store is the Evil Counterpart to McAwesome's. Gustavo, Evan, Rose and Zaph are well-adjusted expies of Galasso, Ethan, Amber and Faz. Ronnie's counterpart is Franklin D. Roosevelt, Ninja Rick's is a pirate, and Robin's is Agatha from her original SEMME team. The others so far don't have counterparts, but Mike moonlights there, and gets drunk to do so, so he's his own counterpart.
Sonichu has a few for both its titular character and the Author Avatar. For the titular character, there's Metal Sonichu and Black Sonichu/Blachu/Blake, though Blake turns good. For the Author Avatar, there's Naitsirhc, whom takes Evil Counterpart to a major extreme.
The titular characters of Bob and George. While George is depicted as god of electricity, Bob is depicted as god of fire. George's "true" form is called Blitz (originally Spark) and Bob's true form is called Napalm. They both got their powers from their mother. In the story, Bob/Napalm calls himself "the destroyer of civilisations" and George/Spark/Blitz believes in justice. Also, in the end, they get help from their respective protectors; Bob from Helmeted Author and George from Shadowy Author. Also, it's revealed that both of them were protected by their mother.
The Author and the Helmeted Author/Fistandantilus are also good and evil versions of each other.