Gendo Ikari. At the start, he keeps it unclear whether he does care about his son, Shinji, and the world's safety or not. In the end, we learn that it's neither, he's just obsessed with bringing back his wife and will use any means to do it, but while he doubtlessly puts getting his wife back before anything else, the way he justifies his actions in episode 25 suggest that he genuinely believes that his version of the Human Instrumentality Project is the only way for humanity to survive, his final words make it pretty clear that he did care about Shinji, but happened to have the very same self-esteem issues Shinji has, and the same can be argued for Rei (given that Fuyutsuki, usually the more moral/sentimental of the two, calls him out on getting to attached to her), and he still opposes the actual villains of the show with the goal of doing what he thinks is protecting mankind, ultimately making him more of a Byronic Hero. ...We think.
Kaworu Nagisa is another example; while he is an Angel and tries to bring about Third Impact, he eventually changes his mind and decides to let Shinji kill him so humanity can live. His motivations have been hotly debated, from interpretations ranging from naive but ultimately well-meaning boy who wanted the best for Shinji to cruel Manipulative Bastard who, when his plans for destruction of humanity failed, settled for pushing Shinji beyond the Despair Event Horizon.
Lelouch fits this trope to a T. How sympathetic and selfish are his goals? And does his goals justify his means of trying to achieve them?
In Yu-Gi-Oh! ZEXAL, the Seven Barian Emperors are supposed to be the villains in Season Two, but despite this, the only one who has ever committed any actions that could truly be defined as "evil" is Vector (other than fighting the good guys, if you want to count that) and the rest don't even seem to like Vector at the best of times. (Gilag hasBrainwashed a few humans into helping him, but even then, this never seemed to cause them any permanent harm.)
This is the whole premise of V from V for Vendetta. Hero or terrorist? Or both?
In Watchmen, it's left largely up to the reader to decide whether Ozymandias' master plan was truly the right thing to do.
Same with Rorschach. He is deliberately left morally ambiguous to let the readers decide whether his extreme methods of fighting evil were necessary or not. Or whether exposing Ozymandias's plan was the right thing to do or not.
Transformers: More than Meets the Eye: Cyclonus and Whirl. The former was a former lieutenant of Galvatron, who quit his service and signed on for the quest, he's distrusted by many of the Autobots, because he killed many during his service under Galvatron. Whirl is a dangerously unstable psychotic who's responsible for the great war, teaching a still pacifistic Megatron a brutal lesson in violence, and was twice voted the Autobot most likely to defect. As the comic goes on, both get Pet the Dog moments (Issue 12 giving them separate ones to the same character), Cyclonus reveals a more soft side, and Whirl is shown to be a pitiable Jerkass Woobie who still has some severe mental problems.
Then there's the Galactic Counsel, a coalition of worlds devoted to peace. They really don't like the Cybertronians, and attack them over a misunderstanding. Such hostility is not unfounded, seeing as the war has laid waste to countless worlds, and before the war, Nova Prime's expansion involved experimenting on other planets and purging organic cultures. Rodimus regards them as fascists, but not all of Rodimus's statements should be taken at face value, how they operate among other cultures remains to be shown
Monster X in The Bridge has shades of this. On one hand he's been the vanguard of a brutal invasion force numerous times and is now currently serving the Big Bad. On the other hand he's a Noble Demon who refuses to harm the defenseless and even saved the life of a pegasus after arriving in Equestria.
Queen Chrysalis is an even bigger example, to the point where, if it weren't for the actual show, you'd think she was always a good guy.
Bludworth, the enigmatic coroner who somehow always seems to know what is going on, in the Final Destination series.
The Old Man who is the boss of Omni Consumer Products in the Robocop movies. Even more so in the TV series.
It was implied that the elderly gas station owner from Wrong Turn may have been involved with the cannibalistic mountain men. The sequel outright confirmed it.
Elsa Schneider in Indiana Jones and the Last Crusade goes back and forth between supporting the Nazis and helping Indiana Jones. Overall, her motive is to get the Holy Grail at whatever cost, and she helps anyone who gets her closer to that goal.
Discworld's Lord Vetinari is a Magnificent Bastard par none, who keeps Ankh-Morporkh's nobles in check through manipulation and intimidation. He is also a former Professional Killer to boot. Apparently, he got into his position thanks to a few well-thought-out assassinations and a firm belief that Humans Are the Real Monsters. He's also the most competent and benevolent patrician the city has ever had.
Severus Snape of Harry Potter fame is the poster boy for this trope. His true allegiance is revealed only after his death. Turns out, he's good.
Dolores Umbridge: in both the books in which she appears (Books 5 and 7), the main characters wonder whether she is actually evil and in league with Voldemort or not. While it's never explicitly revealed, it's implied that she has nothing to do with the bad guys, she's just very unpleasant.
Varys. He's a cunning liar and manipulator who does some villainous things and keeps his motivations ambiguous. He claims that he's working for the good of the realm, and we find out fairly early that he's trying to bring back the Targaryen dynasty. In A Dance With Dragons, however, we learn that Varys went to Westeros with the plan of expanding his and Illyrio's criminal empire. His interest in the Targaryens might be no more noble than Illyrio's: he just wants a big reward.
Tyrion is willing to do a lot of evil things, sometimes purely for his own desires. He also fights to expand the power of his evil family. However, he also seems to have a genuine interest in saving lives and helping those who cannot help themselves. It's unclear sometimes whether we should really want him to succeed, but he's likable either way.
Melissandre. She thinks she's doing the right thing, and is willing to do quite a lot of evil to make that "right thing" happen. However, what she views as "right" might be a bit different from other peoples'. All we know is that some powerful force is backing her, but whether it's truly benevolent, or a god, or even cognizant isn't yet clear.
Youko Tsukimori from the lightnovel Gekkou. The driving question of the novel is whether or not she's a killer.
Mad Oracle Rashk from Glory in the Thunder teaches a runaway boy how to read and gives little intelligent birds as gifts to children. He also makes those birds out of human souls.
Mad Men's Bert Cooper is not afraid to resort to blackmail to get his way, and has threatened to lock someone who disagreed with one of his schemes in a closet for a weekend if he didn't comply. Another character believes that he has arranged for someone to be killed before. However, it is never made clear if he intended to follow through with his threats or if he really had that person killed. He always comes off as a kindly, albeit eccentric, old man.
Sister Jude starts off American Horror Story: Asylum as a Knight Templar intent on literally beating the sin out of the residents of Briarcliff, with a rather loose interpretation of what contitutes "sin" but the revelation of her own backstory, she's atoning for her own sinful life which culminated in a hit-and-run accident involving a young girl plus the far worse people and...things inhabiting Briarcliff move her into this territory making her either an Anti-Villain (combination of Types II and III) or Anti-Hero (Type V).
There's no doubting that Walter White of Breaking Bad isn't a moral person - he cooks crystal meth. However, his reasons for doing so are understandable (he is in a terrible financial condition and he is dying of cancer), and the real question is whether his intentions are noble or not. Early on, it's clear he wants his family to have a stable financial future after he dies, but as time goes on it becomes more apparent that part of the reason why he's making drugs is to get revenge on the society that treated him like dirt for years. His questionable morality serves as a crux for the plot of the story. In the end, he claims that he was really doing everything for himself, though he at least tries to redeem himself in the last episode. However, he is still completely unapologetic about his sins and makes it quite clear he would do it all over again if given the chance.
A minor, but more conventional, example is Herr Herzog, CEO of the large German conglomerate firm Madrigal. While many of his employees are implicated in the drug trade and one of the restaurants owned by the company was a front for drug kingpin Gus Fring, it is unclear if he personally knew about the widespread criminality in his company before it all came into the open. The fact he only has one brief appearance, despite his important position, does not help matters.
The insurance salesman and possible mobster from an episode of The Office
First Enchanter Orsino from Dragon Age II. In the endgame, he admits he knew about the blood mage serial killer who murdered Hawke's mother (and others), but kept his existence secret for fear of the backlash against the Circle. He also claims that he didn't know the extent of Quentin's madness until too late, and never used the man's research until Meredith went completely insane. The writers have said that whether he is telling the truth is left for the players to determine.
Flemeth from both games. She dismisses rumors without confirmation or denial, and there hasn't been a witness to or onscreen demonstration of her villainy. She's done more to assist the heroes, and her battle with the Warden was only in self-defense. Her power is said to come from demonic possession, yet neither her motives nor methods match any other examples. Morrigan discovers a ritual that supposedly permits her to possess others, but the reasons and results for using it have been cast in question.
Her daughter, Morrigan, easily follows in her footsteps. Despite sticking with the Warden for the entire game, her true motives are left in the dark throughout the game, such as why she wanted a child with the soul of an Old God. She can also convince the Warden to slay Flemeth for her to prevent the aforementioned possession ritual, but Morrigan was the only one capable of reading Flemeth's grimoire where the ritual was mentioned, making it possible she lied simply to get her mother out of the way.
In Witch Hunt, Morrigan is initially reluctant to agree if the Warden requests to travel with her, believing that they - especially male Wardens who romanced her - wouldn't agree with or understand what she needs to do to enact her plans.
Ulysses from Fallout: New Vegas is pretty much this. He seems destined to end up fighting The Courier in some sort of legendary battle. Joshua Graham implies that he might have ties to Caesar's Legion. He carries the flag of the Old World on his back, which has connotations, and Old World Blues hints pretty strongly that he wants to do something in The Divide, related to waking up the Old World. Though audio files from the same add-on detail him rescuing Christine from the Big Empty and nursing them back to health.
Eventually, he's revealed to be a Woobie, Destroyer of Worlds of sorts on a Roaring Rampage of Revenge against the Courier for destroying a nation in-the-making, with his ultimate plan being to use ICBMs to cut off the NCR supply lines, leading to the NCR, Legion, and the Mojave destroying each other so that a new nation may rise from the ashes of the Old World symbols.
In Immortal Souls, there's only two things anyone knows for sure about the Black Witch: She's very very powerful, and very very crazy. She seems to do both great harm and great help on a whim, and only she knows what her true motivations are.
Pokémon Black and White's Team Plasma is this for roughly five minutes. Ghetsis' speech does make sense, but they are the shady organization in a Pokémon game. Then we see one of their grunts kicking a Munna. N does keep his ambiguous status till the end when we learn that he's just misguided.
The Spathi of Star Control 2 are a textbook example. They fight for the Ur-Quan and don't seem terribly upset about being party to the enslavement of all intelligent life, but while spineless and shifty they never come close to doing anything evil.
The Arilou are a somewhat more benevolent version. They clearly care about humanity, though their reasons for doing so are left ambiguous. They are also The Greys, and have done experiments on us throughout our history, again for purposes they are reticent to discuss. And while they joined the Alliance, they abandoned it as soon as it became clear that the human race was "safe" (i.e., safely enslaved), and were unconcerned with the fate of their other allies.
The Orz. Weird Starfish Aliens whose language we can't properly translate. They are quite friendly, and will gladly ally with humanity...but there's something a little bit sinister about them. You meet them in Androsynth (evil cloned human) space, with no sign of the Androsynth anywhere. Demanding answers from the Orz as to what happened is their Berserk Button, and they will attack if you keep bringing it up. The Arilou (see above) insist they are dangerous, and vaguely dole out Eldritch Abomination / Cosmic Horror Story implications. It's all surprisingly creepy.
Certain comments made by the Spathi leadership in 2 points to them being quite simply very, very cowardly. They are in fact upset about being party to the enslavement of all intelligent life — not really because they are opposed to enslavement, but because they don't want to risk themselves enslaving others (they actually wanted to be safely protected beneath a slave shield instead, just like the humans would be, but another slave race messed with the choice). Going against the Ur-Quan would be even more dangerous, which is why they keep co-operating.
The Voodoo Lady appeared unquestionably good during most of the Monkey Island games, but some of her actions in Tales of Monkey Island have brought her true alignment into question.
Dark Souls: Most of the big players in the backstory are heavily dependent on interpretation, the codifying dichotomy being that between the two Primordial Serpents, Kingseeker Frampt and Darkstalker Kaathe. Each will have you believe the other is deceiving you regarding whether or not to take Lord Gwyn's place as the fuel of the First Flame. Frampt claims that not doing so will be The End of the World as We Know It, Kaathe claims that letting the fire die will bring about the Golden Age of Mankind and that the current state of affairs are the unnatural extension of the Age of Fire. Neither case has a great amount of evidence to back it up.
Likewise, Gwyn himself is either the long tortured husk of a god sacrificing himself to save the world from the dark, or a selfish tyrant, unwilling to forgo the rule of giants and the subjugation of mankind.
Quelaag, the Chaos Spider, may have been doing all she could to ease the suffering of her younger sister.
Raymond from Resident Evil: Revelations. His first scene in the game makes him look like an antagonist, but he spends most of his screen time as an ally. He seems to be a good guy by the end of the game, and even saves Parker's life, but The Stinger just makes it even more ambiguous.
Everyone in Shadow of the Colossus. It mostly hinges on Dormin's moral ambiguity; if They're evil, then so is Wander for trying to unseal Them, and if They're neutral or good, Emon is evil for violently standing against them, and is still ambiguous anyway because of his implied involvement in sacrificing Mono. If you get into the wild mass guessing about the game Shadow is a prequel to, ICO, even Mono can end up becoming ambiguous. The only character who isn't at all subject to this is Agro, since, being a horse, she's just a loyal steed doing as her master directs her.
Most of the witches in Umineko no Naku Koro ni fall into this category as suits their whims, leaving it quite difficult to tell which if any of them is evil, good or simply in it for shits and giggles. Surprisingly enough, should you have read Higurashi, it turns out that Takano expy Lambdadelta is the one who is actually a decent person and reliable ally as compared to the Rika expy Bernkastel who is only in it For the Evulz.
Of the six members of The Order of the Stick, Vaarsuvius is the most morally ambiguous. Vaarsuvius is condescending and arrogant and doesn't really care much about saving the world; s/he just joined the Order in pursuit of Arcane knowledge and power, and is trigger happy in his/her use of magic. But s/he genuinely cares for the rest of the Order, and is appalled by Belkar's psychopathy. S/he also made a deal with some fiends for some nasty dark magic to save hir family from a vengeful black dragon, but used that magic to destroy the dragon and all family members related to her. S/he then held onto the power and used it to teleport the Azure fleet to an abandoned island where they could establish a base and get supplies, and used the magic to unsuccessfully fight Xykon. This eventually led to hir losing hir temporary power and divorcing hir partner. There is much debate over hir Character Alignment.
Minister Malack, while working with the Empire of Blood and the unashamedly evil Tarquin, is mostly a pleasant guy who treats his differences in alignment and deity with Durkon as more of a friendly religious debate than enmity. He also seems to hold to a personal code of scruples. Turns out he's actually a Vampire and Always Chaotic Evil.
Yokyok of the Linear Guild. For the most part the Guild are Evil Counterparts to the Order, but while their first Kobold member Yikyik was as evil as his opposite number Belkar, it's implied that Yokyok may differ as much in alignment from his party as Belkar does. His only goal is to get revenge for Yikyik's (his father) death by killing Belkar (who has it coming about a hundred times over). Nevetheless, he seems to have no qualms about letting the rest of the guild destroy a whole town if it means he can get to Belkar.
As of late, Durkon the Vampire. He claims to be the same person, but given the way the rules work, one wonders how much of the old character remains and whether or not him continuing along with the rest of the party will cause any issues. Roy, Elan, and Haley all volunteer to help with his need for blood, since anything he drains is easy enough to fix with a single spell.
In Girl Genius, Baron Klaus Wulfenbach starts out as a villain who has conquered most of Europe. The reason he did this was to keep in check his fellow mad scientists, who were mostly waging an everyone-against-everyone war on ruins of a halfway-happened Zombie Apocalypse when he crashed the party.
Jägers are mostly considered nightmarish monsters outside of their masters' land — where they are, conversely, mostly considered heroes. The sorts of people who chose the transformation and indefinite active military service are obviously dangerous, but "good sports" and honorable in their own strange way. Most are not actively malevolent — one is, but he "iz no longer a Jäger". Still, their word for a Heterodyne who choose good over evil is "boring".
King Radical. His actions could easily label him as a Anti-Villain or even an outright hero. Dr. McNinja, on the other hand, is certain that he's a Villain with Good Publicity, and his future self even admitted that he had been planning something big. Just what he's planning, and where it stands morally, though, has yet to be said.
Ava's Demon: TITAN serves as the antagonist of the series. On one hand he's conquered numerous galaxies, and even threatens to destroy all of the planets under Wrathia if she does not surrender to him. On the other his subjects have a decent amount of prosperity, and fairly good medical programs, having saved Gil from death and healed him. Back to the first hand, his empire is set up as something of a Social Darwinist society with the motto "Failures don't get into paradise." Finally, he hasn't appeared in the current narrative, his appearances are told through very biased people, Wrathia, a brutal alien warlord who wishes to take him down and Gil a meek medic who idealizes him.
Jhudora from Neopets. Everyone thinks she's evil, but no one has ever been able to prove it.
On Galtar and the Golden Lance, Rak and his son, Tuk, are mercenaries who serve either Galtar or Tormack, depending on the circumstances.
Zuko from Avatar: The Last Airbender starts out this way. He is the first antagonist, but is given enough sympathy points through out the first season that it is more than a bit hazy on which side of the fence he'll wind up. He ends up choosing evil over good...then, realizing what a mistake this was, chooses good over evil.
The masked and compelling Amon of Book I has a sympathetic backstory told by himself, a number of legitimate points, a mysterious and horrifying ability that he initially only used on the deserving and a meticulous, effortless brand of manipulation that throws everything he says and all his motives into question. While he eventually goes past the Moral Event Horizon (even targeting children), with his public backstory revealed to be a lie (with himself being a Boomerang Bigot), his true backstory is still a very tragic one, andhis brother Tarrlok believes that Amon really does think that what he's doing is the right thing, thus keeping him under this trope.
His Equalistsubordinates belong here as well, despite being relatively minor characters, (there's only four Equalists who have any lines and only two of them actually have names). They do try to eliminate bending from the world, but only in an effort to make things, well, equal. Though many are implied to be merely prejudiced and/or in it primarily for personal revenge, a good percentage of them see themselves as crusaders of justice fighting to reverse the perceived second-class status of non-benders by putting everyone on the same playing field. The Lieutenant in particular becomes very angry when he sees proof that Amon is a bender who's been using his own powers the whole time.
Korra's uncle and spiritual advisor, Unalaq, seems to be taking up this mantle as of Book II, with subtle shades of Evil Mentor and The Fundamentalist, but he ends up going deep into full-out evil territory when he's revealed to be a sociopath working for Vaatu, spirit of chaos, with the intent to plunge the world into 10,000 years of darkness under his rule, though his ultimate intention is to create "balance" by abolishing all nations and rejoining the human and spirit worlds.
Zaheer of Book III detests tyrants, sincerely hopes to create a better world for people to live in, cares quite deeply for his main teammates, and can be quite kind to bystanders (even calling out one of his own teammates for needlessly threatening a radio operator), but he plans to accomplish his goal by killing all government leaders and having the entire world descend into chaos, and he is more than willing to kill both lesser minions and innocent bystanders to fulfill his plans.
On Adventure Time,Marceline was this trope in at least her first few appearances, where it was sort of unclear if she was actually going to start killing people or was just messing with Finn and Jake. More recent episodes portray her as basically good, if somewhat mischievous and perhaps capable of true nastiness.
Peppermint Butler can talk to you in your dreams, likes the taste of human flesh, just mentioning that you know him will get Death himself to do favors for you, and when Finn tried to expose his true aura, he embarrassingly remarked, "You don't want to see that." He's still a loyal butler to his not-evil princess, and occasionally helpful.
Flame Princess. Though she comes from an evil race and has willingly caused massive damage, she does not seem to have any real malice in her actions. Time will tell where she really falls.
Lemongrab. He takes the "Well-Intentioned Extremist" and "Ambiguous Disorder" tropes and stretches them so far that we're not sure if he's evil or just extremely crazy and amoral. The worst thing he's ever done in the show is torture children in an electrical chamber, but it's possible that during this part, he was legitimately insane. He also appears to have a loving family, so it's complicated.
MacBeth in Gargoyles. He's quite ruthless about achieving his goals but his main goal is to destroy Big Bad Demona (and thus himself) and he has his share of Pet the Dog moments.
In El Tigre, Manny Rivera often swings between good and evil. In one episode, a device that detects if a person is good or evil exploded when he went through it.
In Warhammer 40,000 this is the Alpha Legion's hat, down to the last man. While they sided with Horus during the Horus Heresy, they were apparently attempting to fulfill a prophecy in which Chaos would be destroyed permanently (at the cost of the human race albeit). After the Heresy, they're the only legion not present in the eye of terror, and are generally planning something...