The second season of the Gunslinger Girl anime showed the perspectives of the SWA who were trying to protect Italy and the Padanian terrorists who were trying to free their country from an oppressive government.
In the Fullmetal Alchemist manga the near-genocidal Ishval Massacre is told from the point of view of the invading Amestrian soldiers, the Rockbells (heroic war-zone doctors), and an unnamed Ishvalan Warrior Priest (Scar). Nearly all the Amestrian soldiers are shown as disgusted by the orders of the higher-ups, who are mostly remorseless bastards, to the point where about 20% of the Amestrian officers are killed by subordinates tired of killing innocent people. By the end of the volume everyone except the actual villains are traumatized. In one scene Alex Louis Armstrong, mainly a source for comedy relief, is shown having a nervous breakdown right on the field while cradling a dead Ishvalan child.
s-CRY-ed features Ryuho, who is at first supposedly the villain, but throughout the show, both the characters have their heroic and villainous moments. After Ryuho loses his memory and Kazuma goes through a masochistic phase, neither character appears to be the villain. This also happens to Asuka Tachibana, who goes from being a villain talking about his balls to a heroic, lone ranger
Magical Girl Lyrical Nanoha A's does this for the Wolkenritter. While they at first appear to be evil when their motives haven't been revealed, the narrative POV later occasionally changes and focuses on them, their past and such. Turns out they are just trying to save an innocent Ill Girl that showed them what a real family is like.
On the flipside, it seems that part of the Yu-Gi-Oh! fanbase feels that the show's token leather pants wearingAnti-Hero Seto Kaiba would be a case of this if he were the main protagonist, owing to his Dark and Troubled Past, especially since many believe the Pharaoh isn't any better and consider him a case of this trope.
Smug Snake Makoto Isshiki of RahXephon has an episode-long flashback of his childhood living with the Bahbem foundation, revealing a Start of Darkness which makes his child-self a complete Woobie. Although he remains a bastard throughout the series, this insight colours his future actions effectively and makes his motive much more understandable, if not entirely likable.
In any other setting, all of the characters (except Kasumi Tendo and Akari Unryu, both of whom are practically background characters) of Ranma ½ would be horrible monsters who might occasionally do good deeds (some more then others), but are still horrific JerkAsses whose sole good quality is they constantly tear into each other instead of teaming up and wreaking havoc on the countryside. As Ranma 1/2 focuses specifically on them, however, they can come off as amusing, sympathetic, even tragic.
Zig-zagged in Death Note. Light is the Well-Intentioned Extremist protagonist, he is shown to get quite depraved and insane. While the police do their share of morally dubious and illegal things in their pursuit of him.
A large factor of the Magic World arc as a whole in Mahou Sensei Negima!. From Negi's point of view, Fate Averruncus is a dangerous terrorist who is trying to destroy the world. When we see the matter from Fate's point of view, he's trying to stop some brat from interfering with his plan to save over a billion lives in the only way he knows how. Both are right, so they manage to come to a compromise, unlike the previous generation.
It could be argued that Katanagatari is a traditional High Fantasy Chambara sword fights in eighteenth century Japan, but the Sympathetic P.O.V. is from the villains: It’s about the story of the Mooks who look cool for just a moment and is killed immediately by the Antihero. Togame is the Dragon In Chief who thanks she was killed before getting a true chance to become the Big Bad. Shichika is The Dragon. The Big Bad was Shikizaki Kiki, the guy who organized all the plot. Princess Hitei is the Antihero and Emonzaemon is The Lancer. The Evil Plan was stopped. Japan’s true history was restored, and You Cannot Change The Future.
The second and third seasons of Hell Girl swap out the original Black and White Morality of the series for a Black and Grey Morality where neither the victims nor the antagonists are completely in the right. The second season's stories are told through the perspective of the main character Ai, who is in charge of investigating and carrying out vengeance contracts; and the third season focuses on Yuzuki Mikage, who through interaction with the victims and Ai's associates gets to watch her hometown and her life go completely to Hell because of the Hell Correspondence.
The comic Lex Luthor: Man of Steel looked at Superman from the perspective of his archnemesis. Here, Superman comes across as a cold, distant, incredibly powerful alien whose immense natural abilities make a mockery of human accomplishments.
Although in this case, for all his supposed humanism and the angry glowing super-eyes of his rival, Luthor's actions in the comic still make it absolutely clear who the villain is.
Transformers More Than Meets The Eye: The story mainly takes place from the Autobot's point of view, but for two issues it focuses on a team of six low ranking Decepticons trying to get home. They all have sympathetic moments, a few have unsympathetic moments, and they even have interesting conversations about the war.
The Prince Of Egypt does this with Rameses, focusing equally on him and Moses. He's generally shown as a nice guy struggling between responsibility and his own feelings (but with two Evil Chancellors) who genuinely loves his (foster) brother, and doesn't descend into outright villainy until God goes "biblical" on Egypt.
In the movie (well, at least the remake) The Longest Yard, most of the protaganist's football team are self-confessed scumbags and degenerates. The viewers end up rooting for them because the guards are even nastier.
Four Lions is a black comedy from the POV of four Islamist terrorists who are just young guys who happen to want to blow themselves and other people up.
Damsels In Distress: The Damsels - an arrogant clique trying to shape their university to their way of thinking - would be the villains in most other movies but we get to know them and for all their eccentricity and flaws they are deeply lovable. Likewise the dimwitted jocks of the local fraternities are adorable goofs and characters who would normally be heroes in a university story - the editor of the college paper and a depressed goth girl-come across as judgemental jerks.
Notable in the Discworld novel The Truth, in which the protagonist is a journalist who causes some friction with the City Watch (effectively the city's police force). The Watch had been portrayed in previous novels as likable good guys, but here they appear sinister and obstructive, even though they're just the same as they always were.
The later book Going Postal takes the POV of con artist-turned-government employee Moist von Lipwig. From his perspective, the newspaper started by the main character from The Truth becomes little more than a tool to be played with by whoever's clever enough, instead of the struggling moral emblem it was in the previous book. Also, from his perspective, he sees the Times editor William de Worde as a pompous windbag, while in The Truth de Worde is living on his wits and trying to stay a step ahead of his enemies, much like Lipwig does in his books.
And in Thud! we see the trouble both the Times and, to a lesser extent, the Post Office are causing from the Watch's point of view.
Many think that this is Vetinari's doing, since his whole modus operandi for staying in power is that everyone hates him, but hates each other more. And this "hatred" will ensure Vimes, William, and Moist never pool their power together, instead work their hardest to keep each other in check.
Steven Brust does this very well in some of his Dragaera novels. For instance, the leader of La Résistance in the Taltos series was a servant of one of the heroes of the Khaavren Romances, and each is presented as a minor character in the opposite series. Similarly, through Canon Welding, the human hero Fenario, of an originally-unrelated novel based on Hungarian folklore, turns up as the leader of a somewhat unsympathetically-presented rebellion against The Empire in the Khaavren Romances, and ultimately signs a treaty with the hero of that series.
It's a more minor example, but in one instance, Vlad makes a comment about how Dragaerans have no taste in wine, which shows in the fact they call a wide cross-section of beverages wine, and don't differentiate. Paarfli at one point comments on how Easterners have no taste in wine, which he bases on the fact that they oddly decided to give a bunch of names to the same beverage.
The novel Tiassa includes segments from the perspective of Cawti, and she comes across as far more likable than she did in some of Vlad's narration. There's a definite impression that Vlad's bitterness over their break-up meant that his presentation of her wasn't wholly accurate.
Oddly, the story The Desecrator has characters become less sympathetic from seeing their prespective. It's narrated by the Dzur Telnan, and in the story he meets up with/faces off against the skilled magic-user Daymar. While in Vlad's narration, Telnan comes across as a likable ditz and Daymar as an eccentric cloudcuckoolander, in Telnan's narration, he's an Ax CrazyBlood Knight and Daymar is something of a Deadpan Snarker and not afraid to use magic against those who cross him.
Tyrion, who mostly comes across as sympathetic because we see him almost entirely from his point of view. It's easy to forget that he's the same guy who ordered a singer to be murdered and carved up for soup in King's Landing, threatened to rape his nephew to keep his sister from abusing a girl she thought was his whore, murdered the same whore while on his way towards murdering his father, and let his group of thieving, raping barbarians run wild around King's Landing.
Jon, although to a milder extent. The few viewpoints we get on him that aren't from a friend (namely, Theon) describe him as cold and stand-offish.
Jaime, who spends two books cast as a cold bastard hiding behind golden armor before we get to his POV right around the time he starts to defrost and realize his errors. Even if after that, he does threaten to send Edmure Tully — who's already lost his sister and nephew to the Freys turning coat and joining the Lannisters — his unborn child on a trebuchet if he doesn't comply with a truce.
Cersei is actually something of an aversion; while the audience finally gets a look at the childhood prophecy that's shaped her entire life through fear, they also get a look at her utter hostility, such as her silent fury during the marriage of Tommen and Margaery. Even in her own POV, she comes across as rather petty and selfish.
Theon also comes across as a bit of an aversion in the second book. While we see through his eyes his self-pity and the many ways he tries to justify his betrayal and steadily escalating brutality against the people who were once practically his family, his actions kick him seemingly well past the Moral Event Horizon and none of his angst and self-serving rationalizations can change that. Yet, against all odds, A Dance with Dragons seems to be intent on dragging him back across that particular horizon and making him actually sympathetic again.
GRRM pulls a dirty trick with this re: Stannis— throughout the first book, we're told that he's rigid and unpleasant. Then the prologue to the second book sets him up as a possibly-evil Knight Templar. Then, for the rest of the series so far, we see Stannis through the eyes of Davos, who is both the most honorable POV character we still have and probably the person who loves Stannis the most in the Seven Kingdoms (including his wife). So after 900 pages of thinking this guy might be the Big Bad, and watching him let his Evil Chancellorkill his brother, we still can't hate the guy— though to like him is at least equally difficult.
Actually the guy has a sizeable subset of the fandom not just liking him, but worshiping him. This is a guy who burns his enemies alive to appease a god he doesn't even believe in.
Judy Blume's Fudge novels (Tales of a Fourth-Grade Nothing and its sequels) are written from the perspective of Peter Hatcher, an ordinary pre-teen boy who has to put up with such torments as his goofy kid brother Farley (better known to all and sundry, including his parents, as "Fudge") and his Sitcom Arch-Nemesis Sheila Tubman. Blume also wrote a book starring Sheila, Otherwise Known as Sheila the Great, around the time Fourth-Grade Nothing came out.
Ender's Shadow, the sequel to Ender's Game, is mostly from the view point of Bean, whose POV is much more sympathetic and more profound. It's Bean who gives the actual final order of the War to detonate the MD device within the last fighter remaining.
Honor Harrington: The first few novels give the viewpoints of a Punch Clock Villain from time to time. Rob S Pierre and Oscar St Just are given more and more time over the book series, while more minor characters given viewpoints earlier eventually take over. Not only did the former leaders of Haven gain much sympathy, as they were doing the only course of action they thought could save the government, but the ones who replace them are some of the most heroic characters of the series, despite being still at war with the Heroes. Thiessman himself goes from Punch Clock Villain to Worthy Opponent to Cincinnatus.
Each Women Of The Otherworld book is written from a different point of view, so the obnoxious little upstart from Stolen becomes the sincere young woman struggling to fulfill too many varied responsibilities in Dime Store Magic, and the antivillain motivated by greed in Bitten turns out in Personal Demon to have good reasons for his trust issues with the world in general and the former protagonists in particular.
I, Lucifer by Glen Duncan is told from the point of view of Lucifer himself, all whilst he is inhabiting a mortal body for a chance at redemption. It details his take on the fall from heaven and many other aspects of his life. It's a surprisingly sympathetic take on the Father of Lies.
The early chapters of Wolf of the Plains are mostly told from the view of Temujin, who will grow up to be Genghis Khan, but a few segments take the view of Temuge, his youngest brother. When we look through Temujin's eyes, Temuge comes across as a greedy, whiny brat, but when Temuge tells the story, we see him as a poor kid who constantly suffers the bullying of his four older brothers and cruel father.
This happens a lot in 'The Wheel of Time'', often from one chapter to the next. This is most noticeable with Rand, who is increasingly insane throughout the books. In chapters that take his perspective, his actions and decisions make some kind of consistent, if twisted, sense. Conversely, with other characters, his behaviour seems dangerously erratic.
Grendel, a novel by John Gardner, tells the story of Beowulf from Grendel's point of view. Both Beowulf and Grendel are portrayed as monstrous, though since we're seeing through Grendel's eyes, we understand his motivations, but not Beowulf's.
Will Parry of His Dark Materials comes across as very sinister to anyone who doesn't know him well in-universe.
While it's hard to say that any of the characters in the show were sympathetic, this is basically the whole point of The Wire. The show began by examining the Baltimore police's efforts to bring down the drug dealing Barksdale Organization from the POVs of both the police and the dealers, and continued in a similar vein (with a variety of subjects) for all five seasons.
The Lost episodes "House of the Rising Sun" and "...In Translation" recount some of the same events from Sun and Jin's marriage, but from respective points of view. Each character comes across as more sympathetic in his/her focus episode.
Tyrion is not really a bad guy as far as the audience is concerned, but gets quite of lot of opportunities to appear sympathetic.
Cersei. During the two seasons we realise she is trapped in an unhappy and abusive arranged marriage, she is traded like chattle to further agendas of the men in her life and she truly does what she does to further her own family interests. She loves her family, with the exception of Robert and Tyrion, very much. The advice she gives Sansa makes one almost sorry for her.
Jamie is the incestuous, child murdering, oath breaking Kingslayer yet when he talks to Catelyn, he is surpirsingly sympathetic.
Tywin himself gets many such views in his dealings with Arya. We learn of the love he has for his family, the efforts he made to teach his dyslexic son to read and write, the fact that his father had squandered the family fortune meant he had to act the way he did. We see he is for the most part a reasonable man, who also happens to be a complete bastard.
This trope could easily be renamed Lannister POV.
Stannis gets one in a second season episode. We discover about his efforts in Robert's Rebellion and the sufferings and privitations his bore on his brothers behalf and the thanks or lack thereof he got in return.
The main character in Dexter is a murdering psychopath, but comes off as a likable guy because he has all the screen-time.
Not that he's completely unsympathetic, only killing other killers and sticking to his code as best he can. But if the show was called "Doakes" or "Lundy" he would be the Affably Evil morally ambigous Big Bad.
The show wouldn't be called Doakes if they could get away with Doakes, Motherfucker
Some episodes of Criminal Minds give the killer a huge portion of screentime to the point where in a couple, they're more the protagonist than the actual protagonists. Of course, some of those guys are just generally sympathetic anyway, but the bonus screentime certainly helps.
The best example of this is the episode "True Night," in which the perspective is with the unsub probably three-quarters of the time; we never even see the team deliver the profiler, or the witnesses come forward. It is very effective.
The episode "Parasite" is particularly remarkable in this regard: the killer was a horrible person even before he started killing people, but he gets so much screentime that he almost becomes sympathetic.
Angel's episode "Harm's Way" is done from the point of view of Angel's Plucky Comic Relief vampire secretary Harmony, and though she continues to be the Butt Monkey of the episode, also shows why she can't bring herself to trust the more or less reasonable protagonists; from her point of view they're seeking an excuse to terminate any employee of demonic persuasion with extreme prejudice.
Dollhouse is perhaps one of the best examples of this trope, the fact that Topher and Adelle (and all Dollhouse employees) get so much screen time prevents the fact they mindwipe and pimp out "volunteers" for a living sinking in too far. And it is then only their very nastiest acts that horrify the viewers.
Also, take the character of Dominic. It turns out that he's The Mole, trying to keep the Dollhouse in-check to that the technology never becomes out-of-control. However, he's continually painted as the antagonist, showing the power of this trope.
Jack Bauer in the final season after he crosses the line and goes from hero to Anti-Villain Protagonist as his actions in his Roaring Rampage of Revenge are portrayed as anything but heroic, but he's still portrayed as sympathetic, given that he's been screwed over and betrayed so many times he truly just doesn't have any other reason to go on. The same season also has Allison Taylor for the most part, who despite a Face Heel Turn is still mainly seen as a victim of the season's true Big Bad.
For all intents and purposes. Viole from Tower of God is a terrorist fighting a system that is a vast improvement to an earlier state of the world. However, we've seen him come along this path, we've witnessed the events that shaped and broke him and we've seen the faults of the system, so we as the audience are sympathetic towards him, even if he is okay with killing people or ruining them.
The story mode of the old Forgotten Realms RTS game Blood and Magic was based around this. No matter which side of any of the five scenarios you choose, you're always at the very least a Designated Hero. On one end, the first scenario has you control either a king attempting to pacify a country so that his formerly nomadic people could have a homeland, or a champion of the old king, attempting to drive out the invaders. On the other, the last scenario involves either a wizard aiding a village in destroying a regularly occurring demon invasion...or a group of demons fighting off an unprovoked human attack, and discovering a convenient, renewing food source!
Rifts devotes a considerable section of the corebook showing the Coalition States (The Empire) as they see themselves: the sole strong, reliable bastion of civilization in a world of monsters, chaos and confusion.
In Suikoden III, getting all your army's possible recruits by a certain point in plot unlocks a second playthrough of many of the game's plot twists from the antagonists' perspectives. Though Luc still comes off as a whiny git, and anyone that would willingly team with Yuber for any reason probably isn't a nice person.
There is a much better earlier in the game. From Hugo's POV He comes home to find his village in flames. Than his best freind is cut down right in front of him by a knight. From Chris' POV Her men are attacked at what was surpose to be a peaceful truce meeting and are forced to set a fire and escape though a village. On the way out someone attacks her and she kills him before she notices that he is just a kid.
The game TIE Fighter applies this trope to the Star Wars movies: The Empire are the guardians of peace and order, fighting terrorists and Imperial factions.
The Star Wars Expanded Universe takes it even further; there are a lot of books where the Imperial characters who don't jump ship to the New Republic are blatantly evil, but there are also Imperial Worthy Opponent characters who support only the non-evil aspects of the Empire. Some of them, as in Death Star, never even go through a Heel Face Turn because they were never Heels in the first place - and some of those, as seen in Allegiance, don't even defect and join the New Republic. Eventually Supreme Commander Pellaeon actually makes peace between the Empire and the New Republic, and they become two interstellar governments with different ruling systems and an uneasy history.
A campaign of Age of Empires II features Saladin vs. the Crusaders. Another, Barbarossa, at a certain point enters the Third Crusade and fights Saladin. And the expansion of the previous game had four campaigns on the Roman Empire, and another with Rome's enemies.
Iji has the logbooks of the Tasen and the Komato, including such things as one soldier gushing about her girlfriend (Yes "her", you overjoyedYuri Fanboy), and another wondering if he has his gun loaded, because he thought he saw something big right around that corner. They show that not all of the alien soldiers you're killing are heartless monsters, after all. Some of them are, though.
One of the four playable characters in Dreamfall: The Longest Journey is Kian Alvane, a faithful soldier and apostle of the Azadi Empire, which up until that point of the game is seen only as The Empire. His prescence in the game adds shades of grey to the empire's action, both by making the Empire's motivations seem more human, and by presenting a counterpoint to April Ryan's (one of the game's other protagonists and a rebel fighting the Azadi) seemingly-righteous goals.
Used to great effect in Yggdra Union starting in the middle of the seventh chapter, where the game's Grey and Gray Morality becomes blatant. This is the first point in the game where the important scenes starting off each battlefield are shown from an Imperial perspective, and happens to be just in time to make the remaining generals' Heroic Sacrifice moments considerably more poignant.
Breath of Fire IV allows the player to control the God Emperor Fou-Lu, who initially seems like the Evil Counterpart of the protagonist Ryu and the Big Bad of the game. As the game progresses, it becomes clear that Fou-lu is a very sympathetic individual. Subverted in that the real villains of the game are far from sympathetic, particularly the obstensible Big Bad Yuna.
In the jump from Persona 2: Innocent Sin to Eternal Punishment has this with Tatsuya's older brother, Katsuya. He's rather dislikable in Innocent Sin, shown as a distant big brother who puts work before family. However, in Eternal Punishment, he's a kind older brother who constantly worries about his delinquent, rebellious younger brother. What caused this sudden shift? The change in perception of course: in Innocent Sin you're playing from the perspective of Tatsuya, whereas in Eternal Punishment you're playing from the perspective of Maya Amano, who has JUST met him.
Mortal Kombat Vs DC Universe: The characters of both respective franchises, whether they be good or evil, see the other side as alien invaders trying to enslave their world. They all come to their senses at the very last minute.
Halo 4: At the end of Spartan Ops season 1, Dr. Halsey apparently decides to aid Jul 'Mdama's anti-human Covenant remnant, but many people do sympathize with her. She was scapegoated by her superiors, denied information that John was alive, and is imprisoned in the very ship that she helped build. To top it all off, when she is captured by Jul 'Mdama's forces, ONI refuses to let Lasky rescue her and orders him to kill her instead.
In Dr Horribles Singalong Blog, the titular doctor wouldn't be anywhere near so sympathetic from a different angle. Okay, so he has an adorable crush on a girl he barely knows, but he's also a crazy bank-robber.
Or to remove more of the Sympathetic POV, he's a bank-robber who's stalking a girl he barely knows and has got it into his head that she'll be impressed by him being a supervillain.
In Worm this is discussed with regard to Uber and Leet, supervillains who make money selling subscriptions to their internet TV show.
The series as a whole frequently switches between the POV of Aang and Anti-Villain Zuko. This eventually results in the latter becoming The Woobie. Its a rare case where you spend your time both cheering for The Hero and the guy who's trying to defeat him (well, for his redemption).
There is also a scene towards the end of the series from Azula's POV, where we see that she hallucinates her mother, who she argues with about whether or not her mother loved her. It doesn't make her less of a villain, but it still makes her more pitiable.
Some episodes of Liberty's Kids would be shown from the British point of view. It makes it easier to see that they had their reasons and justifications in the whole span of The American Revolution.
This is more often than not Truth in Television. Take any hated or mistrusted group and talk to a person that belongs to it for an hour. You'll often be surprised how many "villains" in the eyes of the media or the general public are not that bad after all.
In other words, a lot of global conflicts can be boiled down (or oversimplifed) to a large-scale Feuding Families situation.
It has been said that no one who is evil believes they are evil. Or, as per Socrates, no one will knowingly do that which they believe is evil. He has a point, especially when human emotion comes into play.
It can be argued that every time you are faced with a temptation and knowingly cave in, you are doing exactly that. On the other hand, most people feel guilty about it in some way.
The True Crime show I (Almost) Got Away With It, about fugitives on the run from the law, does this. They often will show the prosecutor and then will flip to the (now caught) fugitive's point of view. It helps that quite a few of the fugitives are people who committed non-violent crimes.