Stellvia of the Universe is all about this. There isn't even a single negative character in the series — even the aliens are good. Or at least, they expressed regret after slaughtering a Keiti wing almost wholesale.
A's is the example of this trope in the franchise. The only entity that can be considered villainous is a self-defense program of an ancient artifact, which was corrupted long ago under unrevealed circumstances, while the rest of the cast only attempt to do what they believe would be best for everyone and angst heavily about having to hurt others ("It was such a small wish..."). Basically, the Team Nanoha vs. Wolkenritter is a Good Versus Good conflict.
StrikerS seems to feature a straight-up Mad Scientist villain with Jail Scaglietti until The Reveal that he was made that way by a group of old men who spent their youth fighting to stop a senseless, centuries-long war and were desperately seeking a means to prevent such wars from breaking out in the future. There is also the fact that the "Doctor" has a very family-like relationship with his Numbers and not in a Pet the Dog way: even after seeing the error of his (and their own) ways, none of the Numbers turns their back on Scaglietti, continuing to see him as a parent figure.
Lupin III: While the titular character and his gang are criminals, they wouldn't do anything really heinous, so they are definitely not Villain Protagonists, but Anti Heroes, and their antagonist, Inspector Zenigata, is completely heroic, and their relationships can be described as almost friendly rivalry than confrontation between criminals and law-enforcers. Also, if series or movie features really bad guy, Lupin and Zenigata are almost always supposed to make a short-living alliance against him.
Princess Mononoke: Ashitaka was very much The Messiah, but both Lady Eboshi and San had valid reasons for their actions. The enemy samurais seemed to be bad, but then, you feel if they had been explained then they too would have fair motivations.
Kidou Tenshi Angelic Layer and Chobits lack any really evil characters. There are lots of less pleasant individuals, like the cheaters in the former and the outright perverts in the later, but the closest things to villains in the storylines are concerned about victory like the protagonist or are interested in protecting other persocoms from the damage Chi could potentially cause.
In almost any sports manga/anime, there are no villains. The closest to villains are people who toy with or break the rules to achieve victory, as well as people who treat their friends or companions like crap.
In ARIA, the planet Aqua (formerly known as Mars) is populated by nothing but well-meaning, friendly people—or at least Neo-Venezia is. Every time someone seems to act in less than 100% positive manner it generally is only a matter of slight misunderstandings, which mostly get resolved quickly.
Cardcaptor Sakura has no villains either; in the first arc, the Cards are portrayed more as mischievous beings than truly evil troublemakers and are all subject to Defeat Means Friendship, and in the second arc, the "villain" is quickly hinted (and revealed at the end) to be much more of a Trickster Mentor. All the intelligent characters are presented as decent people, which underscores the "Humans Are Good" part of the trope.
Suzumiya Haruhi. There are pretty much no villains, aside from maybe, possibly Asakura Ryouko, and even then she's just a really, really, really far extremist. All forces are genuinely trying to create the world they think is ideal, and only very few seem too extremist for rationality. The Data Entity wants to just "observe"; the Organization wants to maintain the world as it is; the Time Travelers want to keep a Stable Time Loop. Haruhi herself isn't evil, just a Jerkass who wants a little more excitement, and Kyon just wants his peace. Even the Anti-SOS Brigade has somewhat stinted yet good intentions: Fujiwara wants to keep his race from being "slaves to time travel", Kuyou Suou just wants to communicate in the first place, Tachibana Kyouko just thinks the world is more ideal under Sasaki's influence, and Sasaki wants to figure out the truth behind everything. Not to mention the fact that it might even be better for Sasaki to become God.
Gundam Wing seems to like this trope, too, at least for most of the main characters. Save for the few like Dekim Barton, most of the characters desire for justice and peace, despite that their ways of achieving it is questionable, as pointed out by Relena Peacecraft. Fortunately, Everyone Lives except Treize Kushranada, who willingly dies by his own choice, and the world achieves true peace as Relena sees it. This way, Gundam Wing is a total opposite to the Universal Century series.
Seirei No Moribito has a total of two human characters in it whose motivations and methods are presented as unsympathetic, and they're both one-shot. The main conflict is entirely caused by a misunderstanding by the traditionalistic/dogmatic anti villains, and the fact that their cause manages to come across as understandable when it involves child-killing speaks volumes for the tone of the series.
Star Driver is full of this. The Glittering Crux want to use the Humongous MechaLost Technology to achieve world peace (by force, but the force part is only implied and never stated outright.) Many of the Crux deplore loss of civilian life and go out of their way to prepare ways to get the innocent (such as keeping a luxury ship large enough to Cary the population of a small island on hand) out of the way in the event if a crisis. The only reason they're at odds with the heroes at all is the "force" part. Both parties are fully aware of this and even act as genuine friends when off of the battlefield too. There are a total of two characters who's names that we know who're portrayed unsympathetically/as genuinely bad and unlikeable people in the whole of the series, which stands out for it's surprisingly large cast.
Astro Boy: While minor human crooks and such may be genuinely evil, the Big Bad Dr. Tenma and related characters are just Well Intentioned Extremists. If a robot is portrayed as a villain, it's always due to a misunderstanding. This is in contrast to the rest of Osamu Tezuka's work, where pretty much everyone but the main character is always a bastard. Especially Rock.
In Fairy Tail, the majority of the major villains have reasonable and sympathetic motives. The first one is trying to release a monster so he can defeat it, which is the thing his teacher died doing; he merely wants to prove himself by surpassing her. Another notable villain was a slavemaster who spent 8 years building a tower to revive the most dangerous dark wizard in history because he was brainwashed into thinking it would bring about a Utopia. Both of these later pulled a Heal Face Turn. Some later enemies, like the Oración Seis and Grimoire Heart guilds had guild masters and some members truly in the black morality pitch. However, most of the guild members were given sympathetic backstories and reasons for joining these guilds - like how Ultear's entire "evilness" is because of a misunderstanding in her childhood.
The closest things A Little Snow Fairy Sugar has to a "villain" would be Joe Crow, who is not so much that as just a typical bully. Ginger is fairly callous, Basil and Cinnamon are rather mischevious, Greta is a rich snob and sees Saga as a rival, but everyone else in the show is usually super-nice to one another.
Kanon. Not counting everyone who drove Mai away in the past, the worst we have are the Demons, who, despite their destructive behavior, mainly wanted to show Yuichi said past of Mai's and how they came to be, so that he can send a message to her that her constant battle with them can end as soon as she stops fighting. In general, everyone in the show is mostly good, even though a few of them (such as Makoto and Kuze) are Jerkasses in some way or another.
Digimon Tamersproves'' that yes, you can have intense conflict without anyone who is properly "bad." Every Big Bad is actually trying to prevent threats to their worlds, and you can see why they consider the other side to be bad news. Even the final Bigger Bad is just a program acting on its orders; see Gone Horribly Right.
Most X-Men stories where the antagonists are humans or government forces. Barring genocidal maniacs like Reverend Styker, in most cases their motive is simply the belief that mutants should be accounted for in some way.
Gaston Lagaffe. Gaston wants to sleep, have fun, protect the environment, etc., and the people around him want him to get his work done and obey traffic laws. If Gaston thought his actions through at all, there wouldn't be any problems, but of course he doesn't.
WALL-E, absolutely. The villain of the film was a robot that was doing exactly what it was programmed to do by programmers who themselves just had incomplete information, and all the humans soon fell head over heels in love with the world as soon as they were jerked out of their reverie and take responsibility to work to undo their ancestors' mistakes.
Finding Nemo - Dr. Sherman took Nemo because he mistakenly believed he would not be able to survive on his own with a deformed fin, and Darla is a "fish-killer" because she is a child who doesn't know any better. The other antagonists of the film are simply mindless predators. It's worth noting that both Finding Nemo and WALL-E were directed by Andrew Stanton.
The original Toy Story. Sid is a bit of a Jerk Ass, but he's mostly just a boy who likes playing in an unorthodox way with his toys. Unfortunately, the protagonists areLiving Toys. In Toy Story 2, Al is also a Jerk Ass but otherwise is just a bit of a slob. He steals Woody as well, but considering it got him a deal with a museum that could have gotten him hundreds of thousands of dollars, it's hard to not understand why. Note that this trope is completely averted in Toy Story 3 with Lotso.
Close Encounters of the Third Kind - although Roy Neary's wife and kids might not agree about the film having no villains given their distress resulting from his possession. The ETs originally come across as if they're auditioning for The Exorcist, scaring Gillian half to death and then abducting her infant son, although he wanted to go, and they do return him later.
Forbidden Planet. Morbius: it implies that even the worst people have good intentions
Avatar. The Na'Vi are just minding their own business, and the humans just want the planet's resources to ensure their own survival - but unfortunately the diplomacy ísn't working. (Quaritchand his troops are not considered among the Gray, though)
Many Tom Clancy novels feature something like this, especially those which deal with full-scale war, like Red Storm Rising. Usually, the deal is that good, patriotic souls from different countries will struggle with each other because of the actions of one or two people (usually politicians) who are motivated by pride, fear, or ignorance. Although some villains might be delusional beyond reckoning, For the Evulz types are exceedingly rare.
A lot of Orson Scott Card's writing, particularly in Ender's Saga, deals with the idea that no-one is really evil, and it's all a matter of perspective.
Usually. For instance, the Formics are discovered to have attacked humanity because they have a Hive Mind and didn't know each human was individually sentient. On the other end, the Descoladores of the later books are either seeking outright planetary conquest or are just too alien to comprehend. And the Big Bad of the Shadow spinoffs, Achilles, is most definitely evil.
James White's Sector General space hospital series, a deliberate attempt to write Science Fiction with both tension and a murder deficit. Any aliens who may be trying to kill you have just been misinformed.
Every character in Brandon Sanderson's works is revealed to have "good" (or at least sympathetic) motivations for their actions, though he does include a handful of geniune villains for contrast. Perhaps the most spectacular example is the Lord Ruler of Mistborn, who in life is portrayed as pure evil but is gradually revealed after death to be a very human figure who basically had unlimited power dropped in his lap and did the best he could with it while it slowly drove him mad. One of the major themes running throughout all of Sanderson's novels is that "evil" is usually a lot more complicated than people realize.
The majority of books written by Timothy Zahn don't have many evil people at all. He doesn't really set up along the good guys and the bad guys. The Empire is not all bad. The New Republic is not all good. Other people have their own allegiances. Plenty of antagonists on any side are doing what they think will be best in the long run. He does have some actually unambiguous villains, but most of them at least have solid reasoning behind what they're doing. No one ever wakes up and decides to be evil.
Zahn's non-Star Wars fiction tends to have a lot of this as well; The Conquerors Trilogy in particular features a galactic war caused by essentially a misunderstanding. The humans' standard "greet the unknown aliens" transmission is sent via radio, which causes varying degrees of pain for the non-human side of a First Contact scenario, and thus the aliens understandably interpret the greeting as an unprovoked attack. There are at least four, possibly more, distinct factions involved, none of whom act unjustifiably throughout the course of the brief but intense war that follows.
Also, there are plenty of characters who, despite a fall to Dark Side, eventually come to realize the error of their ways.
Averted with the Vagaari, who, as an entire slaver species, are one of the nastier cultures in the Star Wars EU, surpassed only by the Vong and a few others.
Oddly enough, Kurt Vonnegut states in the introduction to Welcome to the Monkey House that this is one of the guiding principles of his work: there are no villains, just people with conflicting interests.
Then again, his characters don't tend to be heroic either. So...
Most of Edgar Pangborn's antagonists are misguided rather than evil, but that doesn't prevent them occasionally causing horrific tragedies. Example: Tiger Boy, in which the semi-wild title character and a friend he meets are killed due to the belief that he is a demon.
Honor Harrington certainly does feature many an irredeemable villain — and some truly, deeply unambiguous conflicts— but it's also at constant pains to point out that this trope is in play most of the time. In fact, the first part of the series (with the Manticore/Haven war) really only has five or so really evil characters, right at the top of the enemy food chain. The many dozens of other Havenite enemies given names and faces all tend toward My Country, Right or Wrong at worst.
Ursula K. Le Guin's work tends to feature this; in fifty years of publishing, only one of her stories(The Word for World is Forest) features an character she described as "purely evil"
Played with in the novel Miracle Monday, where Superman faced The Devil's agent on Earth. While the demon was truly evil (we get to read his thoughts to confirm it) Superman himself holds this belief, and it's because of it that he ultimately wins.
Even corrupt characters often had redeeming qualities. Russel, for instance, is probably the morally second-worst person on the show who isn't one of those briefly appearing or off-screen terrorists mentioned above, but even he won't let the president bomb the wrong country on the mistaken belief that they'd developed atomic bombs of their own in The Warfare of Genghis Khan and is disgusted at hearing on the news about a woman in Turkey being executed for adultery in King Corn. The worst non-terrorist character is Robert Ritchie, who even goes so far as to not seem to feel any sympathy when he hears about a secret service agent being killed in the line of duty ("crime...boy, I don't know"). Aside from some terrorists and homophobic activists, Ritchie's arguably the only complete villain on the show. Even the Christian right are portrayed as low and mean, but not pure evil.
There ain't no good guys, there ain't no bad guys. / There's only you and me and we just disagree.
Table Top RPG
Blue Rose is this. Most of the conflicts in the setting are meant to be resolved (or at least kept from getting worse) through peaceful, diplomatic means - or through carefully measured policing action at the very most.
In one of the many endings for Bio Shock 2, the child you have been taking care of grows up to realize that there is no "evil", only "pain." Because of the mercy you have taught her, she is able to forgive her mother, and live a healthy life on her own.
Metal Gear Solid 4 reveals that most of the villains were actually good people whose plan to make the world a better place did horribly go wrong. Most events of the series were actually the villains' attempts to use whatever means neccessary to correct their mistakes.
Used tragically in Mega Man Zero. In the midst of this rebellion, barring the psychopaths (Copy X, Elipzo, Omega, and Weil), no one on either side is truly evil. The Zero series has some of the most sympathetic antagonists (Harpuia being #1) in the whole franchise.
In XenogearsAnyone doing bad things is just proven to be manipulated by a sort of cross between a crazy computer system and Giant Space Flea from Nowhere. The guy seen as the Big Bad is actually just misguided rather than truly evil and the hero even forgives him at the end, though he refuses to forgive himself. Another recurring antagonist is a sympathetic character forgiven by the heroes and even comforted by them after his defeat. The two warring nations are shown to be full of mostly good people and make peace. Even the leader of the evil empire is actually on your side for the most part. The entire theme of the game in fact seems to be that the goodness of humanity can triumph even in a Crapsack World.
The Touhou series is full of Designated Villains who are unilaterally revealed to be Good All Along by the time the game ends - in most cases, your character has a tea party with the Final Boss following their defeat. Bad Powers, Bad People is completely averted. The only things in the series that could be considered evil at all are the Saigyou Ayakashi, more popularly known as the Cherry Tree of Doom, from Perfect Cherry Blossom (it hypnotizes people into languishing to death under its leaves, and then eats their souls), and the final boss of Subterranean Animism, who flat-out threatens to nuke all of Gensokyo and even then the latter turns out to be under the influence of a temporary but bad case of power induced crazy on top of being much, much more stupid than evil.
Unusually for an Alien Invasion game, Jeff Waynes War Of The Worlds has an arguable case of white vs grey. The humans are fighting for their home and way of life, and the martians are only fighting because their home and way of life is dying. This does, however, lead to some rather nasty Fridge Logic in that whichever race you play as, you are dooming the other to extinction.
Ursula Vernon, creator of Digger, has complained that she can't seem to come up with a real villain, since all of them have reasons for what they are doing and believe that they're doing the right thing. Some of them admittedly think it's the right thing because they're doing it, yes, or that the ends will justify the means, but no one so far is truly evil.
Freefall forgoes villains in favor of lots of geek-tickling tech-talk. Even the Corrupt Corporate Executives tend to be simply narrow-minded and incompetent, rather than willfully malevolent. It's just that they're not smart enough to figure out that AIs have become sentient, and still think that they're just products. It doesn't help that some of the AIs agree.
Gunnerkrigg Court is known for lacking "proper" villains; Coyote is (arguably) more of a general Trickster, and Ysengrin is simply insane. And Reynardine is... who knows? Tom Siddell confirms this in an interview: "There are no outright evil characters, for example, just situations in which a character might act in a way perceived to be evil."
On the other hand, Diego is a pretty evil character. It's bad enough that he causes the death of the woman he "loves" because she rejected him., but then in this comic, when Jeanne desperately comes to him for help, he just smugly smirks at her fear An alternative interpretation is that he is a coward and strongly in denial. He does seem to be horribly broken after Jeanne dies.
Sort of a combination of the whole buffet line. Definitely a coward, but he did it of his own free will, because he's too petty and selfish to think of anything except how she's getting her comeuppance. Then, rather than face his wrongdoing, he goes into denial; it haunts him for the rest of his life and on his deathbed he claims he was forced to come up with the plan by the same men who asked him if there wasn't an alternative at the time.
The first season of Super Friends. There were no supervillains (with the possible exception of the Raven, who put Superman on trial), just Anti Villains who were all doing the utterly wrong thing for what they felt were the right reasons. In the end, they always Saw the Light, Repented for their Wickedness, and never even went to jail.
Phineas And Ferb - While Candace is often the antagonist, she's neither evil nor truly spiteful - only impulsive and a bit high-strung. Heck, even the evil genius has his decent moments! The only really unpleasant people to appear are Doofenshmitz's parents (in his tales of his Hilariously Abusive Childhood) and the drill sergeant from "Phineas And Ferb Get Busted!" (Which was a dream..)
Unsurprisingly present in My Little Pony: Friendship Is Magic. Moments after the climax of the second episode, the goddess of darkness, who is effectively the Big Bad of the ponies' entire mythology, runs crying into a hug with her sister and counterpart day goddess. Who instantly forgives her. Indeed, the worst villains in the first season were Gilda from "Griffon the Brush-Off" and the Great and Powerful Trixie from "Boast Busters", who were both realistic Jerkasses rather than deliberately kid-friendly villains, neither of which learned their lessons in their respective episodes. This changed with the Season 2 premiere "The Return of Harmony", which featured as its antagonist Discord, a trouble-makingReality Warper with a cruel sense of humor. note But even Discord may be an example of this trope, if you interpret his behavior as Blue and Orange Morality. He eventually got reformed in "Keep Calm and Flutter On". Some of the show's conflicts even border on Good Versus Good, like the Dragon from Dragonshy, who was just trying to sleep until Dash kicked him in the face. Averted for Queen Chrysalis who very much an evil queen, and King Sombra.
Kim Possible has the recurring villain Senor Senior Senior. He had (quite likely) built his fortune legitimately: he turns to evil as a hobby (subverting Evil Is Not a Toy), seeing how closely he can mirror a classic Big Bad complete with setting up death traps for the heroes to escape from. In one episode, Sr. Senior Sr.'s fortune is stolen by a swindler, and he tries to get it back by robbing businesses owned by the person who scammed him: meanwhile, Kim attempts to stop him. She is stopped by his son who turns him in, and Kim settles for Senior earning his money back through the reward money that he'll gain for his capture.
In Moral Orel Orel is a genuinely good kid with Incorruptible Pure Pureness. While Moralton has many horrible people (including his own parents), lots of them are sympathetic, most of whom have their own Freudian Excuse. His parents both had issues with their own parents, while Miss Censordoll is pretty awful, she has one of her own it's hard not to feel bad for her when you learn her mother removed her reproductive system. Reverend Putty is a bit cynical and jaded, but he has his own Pet the Dog moments in regards to Orel and his daughter Stephanie. Joe's a brat who bullies Orel and beats up kissing boys but he he's afraid of growing old and didn't know his own mother.