The Goodkind family. A very rich and influential family, they run Goodkind International, Goodkind Research, the Goodkind Trust, etc. They uniformly take the position that they don't hate mutants, they merely understand that mutants represent a terrible threat to baseline humans. Since the Whateley Academy is a high school for mutants, run by mutants, this makes the Goodkinds the bad guys. Only problem? It's clear that many mutants are a terrible threat to baseline humans. The Goodkinds do provide a lot of money for Humanity First! which is full of bigots, but they also subsidize the MCO and direct the Knights of Purity. Still, when all the main characters are mutants, anti-mutant = bad.
They claim that they don't hate mutants, but when you see CEO Bruce Goodkind in private, it's clear that he does. And funding bigots is the least of their crimes against mutants. They also ship children (including their own son) off to be tortured by a Mad Scientist who horrifically tortures mutants, for example. However, other, less influential, Goodkinds are actually considered good, or at least neutral, characters. The MCO aren't particularly good guys either, thanks to rampant dog-kicking; the Knights of Purity are an enigma - it's not clear where they stand with two major characters having an argument about this...
Ayla — nee Trevor, son of the selfsame Bruce — Goodkind, a.k.a. Phase, is a mutant, a member of Team Kimba, and one of the main protagonists. This is relevant because the stories written from his perspective seem to make it fairly clear that the Goodkinds do believe in using their considerable wealth and power responsibly and aren't necessarily bad people at all...so long as you're a baseline human, anyway (it doesn't help the mutant cause that Ayla's own mother is clinically mutophobic thanks to a particularly monstrous supervillain eating her sister alive in front of her when she was six).
As for the Knights of Purity, they're demonised by Chaka for going after Jolt, an emergent mutant, when Jolt could have easily killed someone (electricity powers). Chaka also points out that they have huge casualty rates, but the KoP go after mutants, usually super villains, and so it's not surprising- they contain mutant threats, and sometimes that can't be done without casualties- sometimes they're the only option or the closest one there.
Blue Laser is frequently staked out and attacked by the Commandos (Gunhaver in particular) no matter what they're doing, including shopping or having Thanksgiving dinner. Gunhaver makes a point of exaggerating the "evil" potential of every action Blue Laser takes. Occasionally, Blue Laser does do evil or pseudo-evil things, but more often than not, they're only opposed to the Commandos because the Commandos are the heroes and Blue Laser are the villains.
Sometimes, it turns out that whatever innocuous thing Blue Laser was doing actually was meant to help them crush the Cheat Commandos. Like the time the Cheat Commandos busted in on their grocery shopping; they were out shopping because a computer analysis had determined that the moldy grout in the shower was the reason they hadn't yet crushed the Cheat Commandos. Blue Laser is that kind of villain.
Das Sporking loves pointing them out in works they review.
Mervin notes in her Twilight reviews that the Volturi come off as reasonable rulers whose only rules are 'uphold the Masquerade' and 'don't eat babies'.
ZeldaQueen and Raxistaicho's review of Harry Potter and the Girl Who Lived points out that Dumbledore comes off as less manipulative and more worried for Rose.
In The Real Us, they point out that the Weasleys come off as less 'horrible people' and more 'normal folk manipulated and taken advantage of by the heroes'.
Cao Cao in Farce of the Three Kingdoms. Granted, he does do quite a few awful things, but arguably a lot fewer and with greater justification than Liu Bei. However, everybody in the story is aware that he's cosmically designated to be the villain and acts accordingly, leading to Then Let Me Be Evil at times.
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