Brainstorm and Jack themselves have evil counterparts in the form of Thunderstorm and Shadow, who are one of the series' most competent villains.
Dungeon Keeper Ami has Mercury and Mukrezar - both are physically weak, but possess devastating magical skill, both conquered the Avatar islands, both are resourceful and cunning and use that to win rather than brute strength.
Fallout: Equestria has Lilpip and Red Eye. Both are Stable Dwellers that wish to make Equestria like, or better than what it was before the Great War. They also both represent one of the Elements of Harmony when corrupted.
Red Eye, who gave up every comfort he had to bring some sense of order to the Wasteland, represents corrupted generosity.
Lilpip, who's overwhelming concern for others often leads to self-destructive and irresponsible decisions, represents corrupted kindness.
Lilpip herself lampshades this as she realizes that, though she despises Red Eye's system being built on slavery, it's the first real working infrastructure Equestria has had in hundreds of years. Red Eye, for his part, feels enough mutuality with Lilpip that he offers to abdicate his position to her. It doesn't help that Lilpip is your typical Fallout protagonist (albeit one with exceptionally good karma) and Red Eye is very much an anti-villain compared to other antagonists in the story.
Clash of the Elements: In part 2's finale, Chaos Alex is this to Alex Whiter. Though this is actually Inverted from Chaos Alex's point of view, for he thinks the real Alex is the evil half. Also, the Sin Samurais to the Genesis Samurais.
Eridan ends up becoming this to Nepeta in Herding Cats. Where Nepeta ships her fellow trolls in redrom, Eridan does so in blackrom.
Racer and the Geek does an interesting take on this trope. Service in the Royal Guard or the Equestrian Royal Army, is considered highly honorable by the populace. However, those who do similar work in a private outfit are considered the lowest of the low. Regardless of the actual character of those involved, their actions and motives will be interpreted very differently depending on if they are a trooper or a contractor.
Thanks Kyubey had Juubey as Kyubey's evil counterpart, by having Kyubey have actual emotions and being more forthcoming with information about Puella Magi, and having Juubey act like...well, the canon Kyubey. Juubey got better.
The Zarner siblings, Takko, Jakko, and Zot started out as evil counterparts of Yakko, Wakko, and Dot. They first appeared in a parody of The Powerpuff Girls, where they were created by Pinky and the Brain as part of a plot to Take Over the World. This was their only Season 1 appearance. Even though the Zarners started out this way, they've become less evil starting with their second appearance. They even made it into the theme song! (In Season 1, the 4th section started with "Meet ZakKo, Pakko, Makko, Jot, the Yarners, and Coach Nurse." From Season 2 onward, it went "Meet the Warner cousins, Yarner Twins, the Zarners, and Coach Nurse.") By Season 3, the Zarners have become good friends of the Warners.
Like Naru, Chisato wants to get into Tokyo University. However, while Naru works hard to achieve her goals, Chisato is willing to do anything, including lying, cheating and stealing. She also blames Keitaro cousin, Yoshinari for how she got caught stealing the answers to a test, even though she is the one at fault here. In other words, just like Naru, it's Never HER Fault that she does terrible things and she blames those hurt by her actions.
Kagura, meanwhile, hates men just for being male and loves uses false accusations as 'justification' for viciously attacking them. In the past, this has led to her flat-out murdering at least one innocent victim. Not only does she show absolutely no remorse for this, she continues to insist she was the one in the right — and her father's lawyers kept her from dealing with the consequences. In a dark mirror of how Naru and Mokoto get others to go along with their punishing Mokoto, Kagura has even remained friends with the victim's sister, convincing her that it was just a 'tragic accident'.
Warriors of the World: Soldiers of Fortune has Big Bad Argath Iruvedla being one to Knight Commander Valkron. Both are (or were, in Argath's case) in positions of authority, overseers appointed by their superiors. However, Valkron exploits his rank to save the lives of others and help people while Argath exploited his for his own dark motive of gaining as much power as he possibly could.
Jules Leng is this to Adam. Both are Badass Longcoat-wearing augmented Number Twos to ambitious transhumanist executives, but while Adam always strives to do the right thing even at cost to himself, Jules has few qualms. Possibly none.
Johnathan (sic) Scholar is this to David Sarif. Both are the aforementioned ambitious, jet-setting, smooth transhumanists, but Scholar is an utterly amoral monster, whereas Sarif had the best intentions for Adam and the world. Scholar makes an In-UniverseCounterpart Comparison in chapter 41.
Hidekaz Himaruya once created Darker and Edgier alternative concept art for several Axis Powers Hetalia characters. The fans have built on these drawings to create the immensely popular 2p!Hetalia characters, all of whom have personalities directly opposite to their canon counterparts. For instance, 2p!Britain is depicted as being good at cooking and either always upbeat, but seriouslyunhinged as well. Save for the aforementioned official artwork, the 2p!Hetalia characters are completely fanon.
Xenilla aka Spacegodzilla is one to Godzilla Jr. They are both sons to Godzilla Sr. and have mostly the same powers, but while Junior wants to protect the innocent, Xenilla wants to take over.
Monster X is one to King Caesar. They are both brave and noble men who volunteered to be transformed into Kaiju to protect and serve their people, and when they are not needed, they hibernate in a special chamber. King Caesar is beloved by his people as a friend and guardian, and his chamber is a peaceful sanctuary. Monster X gained a Super-Powered Evil Side, Kaizer Ghidorah, is hated and feared by his people who only see him a dangerous but necessary weapon, and his chamber is a prison.
King Sombra is one to Xenilla of all people. They both have power over crystal and want to take over a kingdom. Xenilla is polite, knows a bit about Pragmatic Villainy, and is implied to be a bit noble deep down. Sombra is extremely egotistical and constantly expresses how much he enjoys making others suffer and die. While Xenilla's crystals can heal and empower people, Sombra's crystals are toxic.
Fallout: Equestria: Snowfall gives us one to Red Eye: (Does it count if both are evil?) The Shadow King, better known as King Sombra. Both want to restore Equestria to it's former glory, both are actively trying to do so, (although Sombra is doing so a bit more slowly) and both are using the main character to do this. The key difference is that while Red Eye is a Well-Intentioned Extremist genuinely willing to make Equestria a better place, to the point that he plans on killing himself so someone like him isn't around to ruin his new world, Sombra is every bit the evil tyrant who appeared on the show, and probably just wants the Crystal Empire back for purely selfish reasons.
In God Slaying Blade Works, Mordred the Black Knight is one to Shirou Emiya. Mordred can perform a Storm of Blades attack that looks like a smaller scale version of Unlimited Blade Works. Mordred also reacts the same way Shirou does to being called a faker, by boasting that a copy can surpass the original.