Arturo Pérez-Reverte created Alatriste because he got tired of reading French and English language swashbucklers where Spaniards only ever appeared as the villains.
After the Epilogue of each volume are a number of mini-chapters showing the perspective of other major and minor characters in the story, showing how they feel about Myne and the events that have transpired in the story.
During the story's first arc, the most antagonistic figure is the Merchant's Guild guildmaster. Benno, the merchant helping Myne recreate items she remembers from her previous life on Earth, hates the guildmaster because of lot of hostile behavior on his part. When Benno's father died, the guildmaster offered to marry his mother while she was still mourning. A few years after that was refused, the fiancée Benno was going to Marry for Love died and the guildmaster offered a marriage to one of his daughters. This was refused as well, but the guildmaster has continued making marriage offers to Benno's family over the years all while being a frequent obstacle to Benno's ventures. In the story proper, the guildmaster agrees to sell Myne a very expensive single-use magic tool in case she has a serious Devouring episode, but lies to Benno about the price so that even if Benno helps Myne pay for it, Myne will be in debt to the guildmaster and have to move to his store to Work Off the Debt induced by the difference. According to the chapter written from the guildmaster's point of view, the guildmaster was genuinely trying to help Benno's family business through tough times with the marriage offers, but poor forethought and timing with the first two resulted in the subsequent ones being mistaken for harassment. His tendency to be an obstacle to Benno's ventures were him keeping him from biting more than he can chew, which he risks doing by selling Myne's products and trying to monopolize him. The ploy to get Myne to join his store was out of genuine care for her her, as it would have made it easier for Myne to secure a contract with a noble that would give her a reliable supply of the magic items she needs to treat the disease that may otherwise kill her (the magic item sold to Myne was from a supply the guildmaster brought for a family member who might need them in the future).
Burning Dragons: In which the dragons are a friendly and intelligent species and Saint George is a homicidal (or dracocidal) maniac suffering from Fantastic Racism.
A character from an alternate universe in Robert A. Heinlein's The Cat Who Walks Through Walls comes from a universe where Albert Einstein is considered to be evil on the scale of Hitler, despite doing the exact same things he did in our universe: She (and apparently most other people from that universe) blame him for the existence of nuclear weapons.
While most series about school show the Alpha Bitch and her Girl Posse as the villains, The Clique does the opposite, and makes them the main characters, exploring the perspective of mean, spoiledbrats.
Day of the Minotaur by Thomas Burnett Swann tells the story of a teenage boy and girl who meet the last of the legendary race of monsters... only to find that he's not so monstrous as the stories suggest. The girl ends up as his lover.
Fred Saberhagen's The Dracula Tape is a story about how Dracula was essentially a nice guy and no one cared. It takes advantage of the original being a Scrapbook Story largely compiled by Mina; in this version Mina was Dracula's ally, and so much of the later book is reinterpreted as her manipulating the hunters by using their sexism against them. It's implied Dracula is not being entirely honest however; the Demeter massacre especially is presented rather unbelievably as one of the crew murdering the rest by sheer coincidence while he spent the whole journey hiding after being spotted on deck.
Barbara Hambly's Renfield tells the story from Renfield's perspective and turns out to be a very odd romance in which Renfield actually survives the novel and gets to live happily ever after with one of Dracula's "wives".
A Betrayal in Blood by Mark A Latham has Sherlock Holmes hired to investigate the true events of the novel, Holmes starting with the premise that Count Dracula wasn't a vampire and analysing everything from there. While Quincey Morris is still a noble man and Arthur Holmwood was just manipulated, the rest of the 'Crew of Light' (as Van Helsing's associates are now known as) all fall victim to Adaptational Villainy; the Harkers are all but explicitly stated as having murdered Jonathan's former employer so that they could inherit the practice, Jonathan's time in Transylvania is attributed to his predecessor Renfield who just happened to have a breakdown while staying with Dracula, Doctor Seward is incompetent at best and sycophantically loyal to Van Helsing at worst, and Van Helsing is a former spy who is only able to teach out-of-date medical procedures due to the favours he earned in his old career, with his vendetta against Dracula being based on nothing more than the fact that Dracula had an affair with his wife (wider political motives are referenced, but the affair is the clear catalyst.
And as if all the above wasn't bad enough? Dracula's affair with Van Helsing's wife resulted in the birth of a son who grew up to be Arthur Holmwood, so Van Helsing manipulated a boy who could arguably be considered his stepson so that the boy would murder his own biological father.
Steven Brust's Dragaera books feature the Vlad Taltos books, in which we see the Dragaeran Empire from the perspective of the outsider Vlad, while The Khaavren Romances feature the perspective of Dragaerans on themselves. The two series do not usually overlap plot events, but some characters do cross over and come across differently. The Unreliable Narrator of the Khaavren Romances, who is a historical fiction author in Vlad's time, is also a factor.
Not exactly a villain/hero perspective swap, but there's more than a few versions of Pride and Prejudice around which are told from Mr. Darcy's perspective on events as opposed to Elizabeth Bennet's. One example is Pamela Aidan's Fitzwilliam Darcy, Gentleman series, which fleshes out Darcy's character and background whilst still remaining faithful to both the original novel and the period.
Flipped by Wendelin Van Draanen is a book about, basically, preteen romance, starting from when the characters were 5. The book is told in two perspectives - that of Bruce's, and that of Julianna's. The two perspectives are distinct in speaking style (and it kinda helps that the fonts are different too).
John Gardner's Grendel tells the story from Grendel's point of view as a sort of Byronic antihero raging against the heavens while trying to figure out his place in the universe. Beowulf isn't even seen until the final battle between him and Grendel. He comes off as a sadistic psychopath to Grendel and when the two fight we see it entirely through Grendel's eyes, during which Grendel begins hallucinating that Beowulf is some kind of angelic but at the same time demonic being.
Jack Vance's books are usually narrated by a stoic, quiet, hypercompetent hero. The Grey Prince, however, is told mainly from the point of view of the love interest and the Dogged Nice Guy—who see the standard hero as an aloof Jerkass.
His Dark Materials, while at first appearing to be a fairly classic fantasy romp, turns into a perspective flip on The Bible. God's really a cruel dictator (or perhaps innocent wimp being controlled by more powerful angels) who are trying to stop freedom and knowledge. The serpent was never really a serpent, but 'dust', matter which had gained consciousness and is helping other beings learn more about the universe.
How To Train Your Viking, a Spin-Off within the How to Train Your Dragon series telling of a certain collection of events from Toothless' point of view.
Marion Zimmer Bradley's The Firebrand tells it all from the point of view of Cassandra, princess of Troy.
The Song of Achilles, by Madeleine Miller, tells it from the point of view of Patroclus, lover of Achilles.
Donna Jo Napoli's Sirena takes perhaps the unlikeliest POV, that of a siren who refuses to lure men to their deaths, but is drawn into the Trojan War anyway.
Incarnations of Immortality: The first five books feature 'Satan' as the (expected) bad guy. Then we find out in For Love of Evil that the current office holder used to be a monk, and he's more concerned about making sure souls go to their proper destination; also, Gabriel thinks he's effective/dangerous because he's not Drunk with Power. With A Velvet Cloak doesn't feature him, but the plot is really only possible because he effectively won by the seventh book....
Matthew Stover's Jericho Moon is an account of a Hebrew attack on the city that would become Jerusalem, as told by the defenders of its Canaanite inhabitants. It is not sympathetic towards YHWH.
P.N. Elrod's King of Shreds and Patches does a perspective flip of Hamlet, presenting the story from the point of view of King Claudius who is innocent of his brother's murder and at his wit's end to deal with his insane nephew.
Lamb: The Gospel According to Biff by Christopher Moore is more of a reimagining than a retelling, but it changes the perspective of Jesus's life from the big J to one of his closest friends who never really made it to apostlehood.
The climactic baseball game at the end of Left-Handed Shortstop by Patricia Reilly Giff is retold from the title character's perspective at the beginning of Rat Teeth.
Loveless: In the chapter "Horny and Confused", Pip texts Georgia about her first makeout session with Rooney before the latter ran away. The short story Hands Against Our Hearts expands on this scene, where its chapters alternate between Pip's and Rooney's POVs.
The Pulitzer Prize-winning novel March tells the story of the father from Little Women - in this book, he is a flawed individual, far from the saintly patriarch that Alcott wrote him as.
Millicent Min, Girl Genius has two. Stanford Wong Flunks Big Time and So Totally Emily Evers, following the perspective of her tutoree and friend respectively.
Presented literally in the Disney book series My Side Of The Story. Each book is actually two books in one—the first half recaps the events of the film in question from the perspective of the title character, and the reader then physically flips the book over to get the villain's version of the same events.
Never Never, a short story by Bruce Glassco, is the story of Peter Pan from Captain Hook's perspective, where he and his crew are trapped in Neverland unable to win, and Tinkerbell brings them back to life (described in graphic detail) every time they die. Oh, and one of them always Comes Back Wrong.
Terry Pratchett's Night Watch Discworld is a typical Discworld take on Les Misérables, which flips the perspectives of the two main characters, while keeping them easily recognizable. This is made possible because Vimes (Javert) is a much more developed character and his sense of justice is not quite as unforgiving as Javert's, while Carcer (Valjean) is a homicidal psychopath who only thinks or appears to think that he is the wronged, noble hero of Les Miz. As such, Vimes is the one who falls in with the revolutionaries, while Carcer takes to the vicious secret police like a duck to water.
The Truth, Going Postal (and Making Money) alongside Thud! portray protagonists from one book as, well not really antagonists but nuisances towards the protagonists of another. We KNOW Vimes is a Jerk with a Heart of Gold, but in The Truth he wants the paper shut down because it stirs things up, plus he'd probably want to see Con Man Moist von Lipwig behind bars...
Paint Your Dragon by Tom Holt takes the general idea of 'St George vs the Dragon', and makes the point that (despite being part of the official 'Good' side) George is pretty much an evil, despicable man who likes to kill things.
Paradise Lost retells the Bible with Satan as a fairly sympathetic character.
Poster Girl Is a Dystopian novel that unlike most of it's kind, which usually follow the victims/rebels of such a society, is told from the perspective of the regime’s elite, after the revolution has overthrown them. Specifically Sonya Kantor, the titular Poster Girl who appeared on propaganda posters of the tyranical Delegation.
Margaret Atwood's The Penelopiad retells The Odyssey from the perspective of Penelope, Odysseus's wife - from beyond the grave, no less. Perspective Flips also play an important meta-role: while Penelope is waiting for Odysseus to return, stories of his doings trickle back with different spins on the same event, such as whether the Cyclops was really a one-eyed giant or just a half-blind innkeeper pissed off that the sailors wouldn't pay their tabs.
In the Professor Moriarty series by Michael Kurland, beginning with The Infernal Device, Moriarty is portrayed as a long-suffering antihero/hero who patiently endures Holmes' delusions about the extent of his "criminal empire".
Stephen R. Donaldson's The Real Story features a perspective flip, not as a binary reversal of hero/villain, but a more complicated flip in which the victim, the villain and the rescuer ALL swap places. The villain becomes the victim, the victim becomes the rescuer, and the rescuer becomes the villain.
Fred Saberhagen did Perspective Flip novels about Frankenstein's monster and the Minotaur.
French novelist Anatole France wrote a story titled The Seven Wives of Bluebeard which is told from that character's perspective, portraying him as a nice guy whose wives died not by his hands, but by circumstances of their bad choices (one's an adulteress, another a drunkard, etc.). Like The True Story of the 3 Little Pigs mentioned above, the number of "accidental" deaths occurring in proximity to the supposedly innocent protagonist definitely suggests an alternate interpretation that he is an Unreliable Narrator.
Neil Gaiman's story Snow, Glass, Apples turns the evil queen into a benevolent ruler and tragic hero, Snow White into an insatiable vampire that has killed many people (including the king), and the prince into a necrophiliac who fell in love with Snow White because she's basically a walking corpse. Similarly, he wrote The Problem of Susan as the The Last Battle from the point of view of the girl who didn't return to Narnia, and A Study in Emerald as a two-fold flip: a Sherlock Holmes story where the main characters willingly serve Lovecraft's abominations, and are actually Moriarty and Moran tracking the murderers Holmes and Watson.
Shel Silverstein's "The One Who Stayed" (from Where the Sidewalk Ends) is a take on The Pied Piper of Hamelin from the perspective of one of the children of Hamelin. They recall all the other children following the piper over the hills, never to return. The narrator is the only one who did not follow the piper — they heard his music, but were too afraid to follow.
There are a lot of Star Wars Expanded Universe novels that fit this trope, including the "Tales of The" books, each containing several short stories about just about every character who appears in the Mos Eisely cantina and Jabba's palace.
Death Star is popular too. It's about various people on the first Death Star, from Darth Vader on down to a political prisoner whose experience in architecture let her work on the superweapon's less essential elements. Only one Rebel character gets named at all, and that's Princess Leia, who leaves a major impression on the surgeon who tended her after she was tortured. The novel serves to make things a little less black-and-white than in the film; although the Empire is still incredibly evil, it's easier to see why anyone worked for it.
Quite a few characters take rebellious actions, without joining the Rebel Alliance.
The two-part The Sundering series by Jacqueline Carey is a lawyer-friendly inversion of The Lord of the Rings. It's told mostly from the perspective of the Forces of Darkness, who really just want to be left alone and aren't responsible for the cataclysm that has been blamed on them.
In A Tale of the Wicked Queen, the Queen delivers her own alternative interpretation of Sleeping Beauty. In it, Maleficent was a shy, misunderstood woman who feared rejection. She shut herself away with only blackbirds for companionship. Maleficent put Sleeping Beauty into her sleep in order to protect her from the world.
A Tale of the Beast Within reveals the descent into darkness that made the Prince the Beast before love redeemed him.
The Testament of Judith Barton by Wendy Powers and Robin McLeod retells the story of the Alfred Hitchcock film Vertigo from Judy's perspective. It tells a little bit about her background in Salina, Kansas before her move to San Francisco, how she began to take classes on Method Acting, and how she got lured by Gavin Elster into playing his wife Madeleine because he tells her that Scottie was an unstable stalker and that Judy wasn't Gavin's mistress.
A Thousand Acres by Jane Smiley is a reversal of King Lear, set on an Iowan farm and showing the story from Ginny's (Goneril's) perspective.
The Three Musketeers by Alexandre Dumashas been retold from other characters' perspectives several times:
Yes, That Same Milady by Yuliya Galanina is another retelling - from the point of view of... well, Milady de Winter. Yes, she turns out to be very much alive. And, yes, she's an extremelyUnreliable Narrator, and doesn't even try to deny it.
Tiffany Thayer's Three Musketeers and a Lady does a brilliant Perspective Inversion of the story from the same perspective, depicting Milady de Winter as a Tragic Villain who found true love too late.
Till We Have Faces, by C. S. Lewis, plays with this trope in quite a few ways. It retells the myth of Cupid And Psyche from the perspective of Orual, one of the "wicked" sisters. The events of the story are mostly the same, with the biggest difference being that, in the original story, Psyche's sisters could clearly see the fine palace she shared with Cupid (and thus their later actions were clearly motivated by jealousy), but in Faces Orual can't see Istra's palace, making her motivation much more ambiguous. As Orual tells her story, she claims that her first motivation was always Istra's well-being, and she blames the caprice of the gods for the disasters that come from her own attempts to do the right thing. (Istra is still just as incorruptibly pure as Psyche was in the original.) The perspective flip even happens in-universe: Orual lives long enough to hear Istra's story pass into myth, and she's angry as hell to find out that she's become the villain of the story. Then the perspective gets flipped again. In the process of telling her side of the story to set the record straight, Orual has a Heel Realization and understands how much of her "concern" for Istra was actually selfishness.
Peter Watts' story "The Things" is the film The Thing (1982) from the creature's point of view. The "Thing" believes itself benevolent but grows gradually less so - partly because of the blind unreasoning hostility of the world it encountered, and partly because it takes on characteristics of those it assimilates.
The True Story of the Three Little Pigs is narrated by one "A. Wolf," who explains that the huffing and puffing was actually a bad case of hay fever, and he had no big bad intentions against the pigs. "I was framed," he laments. He's heavily implied to be an Unreliable Narrator, however.
The Warrior Cats series does this a few times: Bluestar's Prophecy, Crookedstar's Promise, Yellowfang's Secret, and Tallstar's Revenge all take place during roughly the same time frame, so there are several scenes seen from different points of view - for instance during battles, the cats who are launching a necessary preemptive attack in one book are seen as vicious invaders in the other. Later novellas repeat previous scenes in similar ways, and Battles of the Clans even has twin stories in it that show the aftermath of the same battle in two different Clans, to show that each battle fought has an impact on everyone involved and even on the future of each Clan.
Wicked is a Land of Oz based book (with heavy MGM influences) from the viewpoint of the Wicked Witch of the West (named "Elphaba Thropp"). The wizard is the Big Bad. A major difference is that Dorothy intends to apologize to the Witch in the end, while in the original book, Dorothy and company intend to kill the Wicked Witch, though only succeeded by accident.
The 18th century writer Voltaire had an early example with his story The White Bull, most of whose protagonists are villains from The Bible. The heroine is a Babylonian princess in love with Nebuchadnezzar II currently turned into a bull by God. She is aided in her quest to change him back by a Eunuch and Good Chancellor who was one of Pharaoh's magicians who challenged Moses, his friend, an old woman who was the Witch of Endor, and the Author Avatar, a friendly talking snake.
The Doctor Who Expanded Universe novel Who Killed Kennedy examines the myriad alien invasions and whatnot of the Third Doctor era (1970-1974) of Doctor Who on television from the perspective of a New Zealander journalist named James Stevens who is trying to expose a secret organisation called UNIT and its "Doctor" agents. Stevens is the protagonist while the Doctor himself is barely featured at all, though he is mentioned throughout.
Wide Sargasso Sea, by Jean Rhys, does this for Jane Eyre: Bertha Mason, Mr. Rochester's crazy first wife, is the main character, and Rochester is the villain.
Wings of Fire is a perspective flip on traditional tales featuring dragons. The main characters are all dragons who view humans as little more than cute critters - and many other dragons in the series have even less flattering views.
Polish writer Andrzej Sapkowski is well-known for using this trope in his short stories about The Witcher. In Lesser Evil (Mniejsze Zło in the Polish) we have another example of using it on the classic "Snow White" story - good queen saw terrible things that would be done by her step-daughter in future, and gave orders to kill her. Girl killed queen's servant when he tried to rape her, and ran and joined a bunch of gnomes, with whom she was robbing people. Queen sent a wizard that killed all the gnomes and imprisoned girl in a crystal. But then some stupid prince freed and married her, and she murdered him to rule herself. Then she attacked her family lands, and killed the queen, formed a group of murderers and came to kill the wizard, only to die from the hand of the Witcher. And that's only one example.
The Witch World anthology Tales of the Witch World begins with Andre Norton's "The Shaping of Ulm's Heir"; it is immediately followed by Robert Bloch's "Heir Apparent", in which the same story is retold by one of the antagonists, who naturally gives it a different slant.
from the perspective of the centaurs.