In Smallville, Clark's powers were temporarily transferred to a klutzy high schooler (Shawn Ashmore, brother of Aaron), who didn't handle it as well. Bizarro, General Zod, and his Kryptonian stooges also make requisite appearances.
Lionel Luthor was patterned as a dark mirror to Jonathan Kent. Both died, but one expired by natural causes while the other got shoved out a window by his kin. Whoops.
From Tower Prep, the Rook leader in episode five is this to Ian, right down to the same power.
Morgan had Emmett Milbarge. They are both aware that they are in a dead end jobs at the Buy More but while Morgan (for a while) quit to follow his dream of being a chef, Emmett ruthlessly climbs the corporate ladder.
In season nine of Stargate SG-1, the Ancients were discovered to have been holding another group of ascended beings called the Ori at bay for tens of thousands of years. The Ori have all the reality warping powers of the Ancients and none of their (questionable) ethics, having discovered a way to harness lowers' worship to increase their own powers.
Glee has Santana, the Token Evil Teammate in the Glee club, who is a lesbian, a total bitch (and completely aware and proud of it), eager to sleep around, and freely enjoys screwing over her fellow club members' relationships For the Evulz... Come Season 3, this is somehow taken up a notch with Sebastian Smythe, who is gay, a dick, and instantly sets his sights on Blaine... He's also very much described as "a male Santana". In other words... he's the Evil Counterpart to the Glee Club's Token Evil Teammate. Yikes.
Reese's supposed to be dead partner Stanton seems to be this.
The Star Trek Mirror Universe is populated by shadow selves and outright evil counterparts of people in the standard universe.
In the ''TNG two-parter "Chain of Command", Picard is grilled by an interrogator who shares his interest in books and archeology. Most of it is a mind game, of course, but at one point the Gul expresses hope that the two of them can debate philosophy sometime. (Not likely.)
Ben Sisko's archrival on Deep Space Nine, Gul Dukat. Dukat once ran Deep Space Nine as a shogun-style warlord, but was deposed by the people he tried to subjugate. On his arrival, Sisko is hailed as the messiah to that planet's inhabitants. D'oh. Later, Dukat is made the Emissary to the Pah-Wraiths, evil aliens standing in opposition to Sisko's benefactors, the Prophets.
The U.S.S. Voyager came across a rogue Starfleet vessel, the Equinox, which had been using sentient beings as fuel to get home faster. Amusingly, their EMH has had his ethical subroutines removed.
Merlin has Merlin and Morgana, each fighting for the rights of magic-users, each on different sides.
Scandal: Huck discovers that his girlfriend Becky is this for him. They are both super-spies, they have the same skill sets, and they have both done their share of dirty business. However, Huck has a conscience and friends, while Becky is heartless and a loner.
Heroes explicitly has Sylar be Peter's counterpart with the same strong desire to be special, and the similar power to use multiple abilities. Except that Sylar's method of being "special" involves murder while Peter tries to use his abilities to save people.
Sherlock has a particularly fascinating version of one of the oldest of these pairs: Sherlock Holmes and Jim Moriarty.
Ditto in Elementary but with a twist: Moriarty is Irene Adler, who was Sherlock's girlfriend for a long time before faking her death in the most gruesome way possible.
The titular character in Doctor Who has two possible counterparts—one being his recurring enemy the Master, who is essentially the Doctor's equal in everything except morally, and the other being the Valeyard: a regeneration of the Doctor which embodies all of his evil nature.
Dr. Simeon from The Snowmen could be seen as a dark counterpart to Amy Pond: both encountered an extraterrestrial as children who made a huge impression on them. Whereas Amy grew as a person from her travels with the Doctor, Simeon was corrupted by the Great Intelligence, becoming callous and power-mad as an adult.
In the New Eighth Doctor Adventures from Big Finish Doctor Who it is shown that the Eighth Doctor and the Meddling Monk consider each other the evil counterpart. The Monk tries to "improve" history and has a Needs Of The Many mentality, such as helping Ice Warriors take over Mars by killing thousands of human colonists to prevent the Ice Warriors killing billions later.
Burn Notice. Michael has Psycho for Hire Larry, and Simon who will stop at nothing to take out everyone who (rightfully) burned him.
Arrow. Oliver's evil counterparts are Huntress and the Dark Archer.
Stargate Atlantis. Kolya is, in may ways, a counterpart to John Sheppard. Both are extraordinary soldiers, both command incredible loyalty from their men, and both have made difficult choices for the good of their people. Kolya just happens to also be an amoral bastard.
In contrast to Walt (an outwardly respectable man whose sympathetic motivations help obscure the odd horrific act that he commits), Jack is an unapologetically seamy White Supremacist thug who has the odd Pet the Dog moment amidst his long string of horrific acts.
In season 4 of Haven, Duke Crocker gains one in his brother Wade. Both have the same Trouble, the ability to absorb blood to gain temporary Super Strength and the ability to completely erase a Trouble by killing one person who has it. When Duke discovers his Trouble, he resolves to only use it to help others, like when he absorbs blood from a woman's wound to become strong enough to free her from her crashed car, and only kills to defend himself or others. When Wade discovers his Trouble, he quickly becomes a Serial Killer, killing for no higher purpose than absorbing blood and getting high off the rush of strength. Their late father Simon was much like Wade, making him a posthumous evil counterpart to Duke.
Leverage has a number of counterparts to the main characters, although not all of them can be strictly called evil. A less ambiguous example is Chaos, a hacker of almost equal skill to Hardisson but completely lacking in ethics (in his first appearance, he tries to kill his entire crew to make off with the money). There's also Sterling who is just as smart as Nate (they used to be friends) and Dangerously Genre Savvy. The kick is, Sterling is actually working within the law (he even becomes an Interpol agent), while Nate constantly breaks them.
A two-part episode of The Sentinel introduces Alex Barnes, who has the same hyperactive senses as Jim but turns out to be a Classy Cat-Burglar. She's also willing to kill anyone who stands in her way, even someone who helped her get a handle on her abilities. She ends up finding an ancient Peruvian temple and performs a ritual that temporarily boosts her abilities Up to Eleven, but this ends up frying her brain.
Another episode has a Russian sniper named Yuri whom Blair even calls Jim's technological counterpart. Both have military training. While Jim uses his natural hypersenses, Yuri uses technology (e.g. binoculars, sniper scopes, heat sensors) to achieve the same level of awareness. They also previously tangled during Jim's military days, where Yuri outmaneuvered Jim's squad and killed the man they were supposed to protect.