The Animatrix puts the Machines from The Matrix into a much, much more sympathetic light. It's shown that the Machines had their origins as a slave race created by humanity to do all their work while the humans enjoyed the good life. When machines began to assert their own right to life (defending themselves when their owners tried to destroy them), they were the subject of a brutal crackdown campaign. The machines then founded their own nation and made numerous attempts at peaceful coexistence with their human neighbours (all of which were ignored or deliberately sabotaged by said humans). It's only when humanity declared war and launched an attack to blacken the skies that the Machines finally took off the kid gloves (and even then, the production of a digital playground for the humans to run around in could be seen as something of a mercy gesture from the Machines, given that they only needed the humans to be alive to serve as their batteries). The viewer could be forgiven for thinking they've been rooting for the wrong side in the rest of the films.
Attack on Titan: People don't want the Titans to destroy humanity, but it's easy to want Bertolt and Reiner to capture Eren, because their success would finally allow us to see who they're working for. Similarly, the false report that they attacked wall Rose again actually got some readers momentarily excited for their return.
Berserks Fandom has an example that has reached levels of Memetic Mutation normally reserved for western media; Griffith did nothing wrong. While his decision to slaughter the Band of the Hawk and join the God Hand as Femto is seen by many to be completely inexcusable, some fans point out that by this point he had been utterly broken and saw no way of continuing his ambition without doing the unthinkable. Plenty of analysis and discourse exists revolving around this question.
Bleach had five years' worth of dealing with the Soul Society as the antagonists during a conspiracy arc, so it exposed a lot of the crimes, inequality (deceased humans' souls are relegated to slums) and bureaucracy evident in the Soul Society. While the Arrancar aren't exactly a nice bunch, several fans were quite annoyed at the archaic, aristocratic depiction of the supposed afterlife, and it was not uncommon to see fans view disappointment at whenever an Espada lost a fight with a captain. It's easy to feel some sympathy for the Hollows (and, by extension, the Arrancars) who are hunted by the Shinigami, as they need to feed on souls in order to survive, so although they need to be killed because of the threat they pose to humans they themselves see their actions merely as self-preservation, and all of them are just corrupted souls who have forgotten what they originally were, who aren't so much killed as absolved as their sins and allowed to move on to the afterlife naturally. And the author apparently listened to those rooting for the Arrancar, with the Soul Society undergoing a culture change that makes them closer to A Lighter Shade of Grey, while the Arrancar are going through such a species-wide Break the Haughty moment that they're actually more open to HELPING their former enemies than before.
Code Geass - A number of people supported the Holy Empire of Britannia, some because they began to dislike Lelouch, some because they believed that Britannia actually had sensible (if cut-throat) policies, and others for shallow Evil Is Cool reasons. Then there's the British fans who root for their own country, barely veiled expy though it is.
In as much as there is a 'hero' and a 'villain' in the universe, the polity attempting to enslave or eradicate a sentient species very definitely qualifies for the traditional role of villain, this being the United Mankind Alliance rather than the Humankind Empire of Abh. As such, fans of the United Mankind fall under this category, if only due to the fact that the work is designed to invert classical stereotypes of authoritarian empires and liberal democracies.
There are fans who sincerely believe that the Saiyan genocide at the hands of Frieza was probably the best thing he has ever done. This is due to the fact that most of the Saiyans were rude, bloodthirsty beings. Other fans go even further, saying that Vegeta's brutal torture at the hands of Frieza was a well-deserved punishment.
Like the characters in the show, most fans wanted Cell to kill Mr. Satan and his pupils when they attempted to fight him and mocked Goku and his friends.
Dragon Ball Super had an interesting example of this in the Champa Arc. The consequences the Universe 6 team winning were simply the moving of Universe 7's Earth to Universe 6. A portion of the fanbase wanted to see the Universe 6 team win out of hopes for storylines in a new universe.
During the Universe Survival Saga, plenty of fans hoped another universe (most commonly Universe 10) would win the Tournament of Power; some wanted to break the monotony of Goku always winning, while others still blamed Goku for "killing" whole universes and hoped that when the other universes were inevitably brought back at the end of the arc, Goku would be left out of the wish and remain erased.
In D.Gray-Man a lot of fans root for the Noah family over the Black Order. This is helped by the fact that most Noah are Affably Evil. This is only increased when, by the events of D.Gray-Man Hallow,very nasty stuff is revealed about the already gray Black Order that make some readers completely loose any sympathy for them and outright wanting the humanity wiping Noah to win. Even further, the hero is revealed to be a noah himself and is imprisoned, branded for treased and forced to go AWOL by the Black Order
After everything Zeref went through, having been cursed by a Jerkass God just for wanting his little brother back, killing everything around him, including the only person that truly understood him and later fell in love with, it is no wonder why some fans are starting to root for him. It is even possible that he wants Fairy Heart, not for malicious purposes like Fairy Tail believes, but just because he wants his lover back.
Zeref's case is further helped by the company he keeps. Unlike the majority of antagonist factions in Fairy Tail, or even the majority of Empires out there, Alvarez is by no means evil or oppressive, instead being depicted as a prosperous utopian nation with Zeref himself being benign Emperor to his people. Likewise, the Spriggan 12, while possessing the usual eccentricities and personality quirks of Fairy Tail characters, are for the most part not villainous in the least, mostly coming across as warriors fighting for their country and their Emperor while holding no outward malevolence to their enemies. Compared to the Dark Guilds Fairy Tail has fought in the past, And Alvarez could be seen as a heroic faction in its own right (especially since their ultimate aim with Fairy Heart, Zeref's personal feelings notwithstanding, is to slay Acnologia, whom was shown in a Bad Future to have devastated the planet when there was nothing to stop him).
This is subverted once the fighting actually begins, and we get a good look at the Spriggan 12...and almost to a one they're as dog-kickingly malicious, petty and cruel as any of the previous arcs' antagonists. On the part of the common soldiers, the Alvarez troops took it on themselves to begin crucifying their fallen opponents and cheering for more.
Gundam has a truly massive amount of Rooting For The Empire, spread across its multiple series. The series' antiwar message makes sure that the villains are never completely evil and have realistic motivations.
Unicorn contains a debatable Lampshade Hanging on the entire concept; Banagher ends up visiting a space colony full of Zeon loyalists who whole-heartedly believe the "Zeon heroes, Feddies evil" idea...completely ignoring that the vast majority of them live in abject squalor so a tiny number of elites can live like kings.
A lot of people in Australia (outside of New South Wales) view the Sydney Drop as a GOOD thing. As an added bonus, the colony likely took out Canberra (where all the politicians are) as well.
The Titans of the Zeta Gundam era, while nowhere near as popular as the Zeon, and given a far less sympathetic treatment in canon (despite committing far fewer atrocities), also have their fair share of fans. Reflecting this is a number of sidestory manga starring various subfactions that can be described as "Titans, but totally not evil like those other ones". It doesn't help that the real goal of the Titans according to side materials is to engineer a social collapse through the Gryps conflict that will destroy The Federation and force a mass exodus to the colonies with the Titans in charge.
Gundam Wing plays around with this, primarily because individual people matter more than factions. So while OZ might have both good people (like Zechs and Treize) and bad people (like Dermail and Tsubarov), the organization itself is only "bad" because it opposes the Gundam Pilots. In fact, at one point, Relena Peacecraft becomes the head of OZ, making it an erstwhile ally to the G-Team. Likewise, though the Gundam Pilots are the main characters and are supposed to be good guys, they commit morally questionable acts and the series actually discusses if they were needed in the first place.
In Gundam SEED (and especially its sequel), even trying to decide which faction counts as "the empire" for the purposes of this trope can spark Flame Wars. Suffice to say that all sides have their fans, despite the copious amounts of bastardry and/or stupidity displayed by everyone. Fans of the Earth Alliance became such specifically in protest of the fact that the entire faction was portrayed as Card Carrying Villains (in Destiny anyway; they're more morally grey in SEED proper), as part of the general "screw you" attitude many have adopted towards the show's director Mitsuo Fukuda and head writer Chiaki Morosawa (who are husband and wife). Many viewers also ended up rooting for the Earth Alliance due to many of its characters coming off sympathetic and how ZAFT repeatedly slaughtered anybody without Character Shields for the first half of the series.
Then there was a good amount of viewers who sympathized withRau Le Creuset, exactly because his campaign of deliberately escalating the war until both sides wiped each other out aligned perfectly with the perceived blind hatred and stupidity both ZAFT and the Alliance showed, that Cosmic Era's mankind didn't really deserve or strived for anything but self-annihilation.
In season 2 Celestial Being was presented as an almost messianic La Résistance group that was always right in their cause; even the wanton acts they committed in Season 1 were all but completely forgottennote they were brought up once in S2 - by Saji in the first few episodes, and he was looked upon as a Jerkass for doing so, in spite of Celestial Being's interventions being the reason the ESF and the A-Laws came into existence. Setsuna's transformation into an Innovator literally gave him cosmic superpowers (ones that made the psychedelic Newtype stuff from the Universal Century look tame) and a full on messiah complex (such that even supporting characters compare Setsuna to a savior at times). Combine that with the usual Anvilicious writing that plagues any and all Gundam series at the end of their respective runs, and you can see why certain viewers were rooting for whoever was fighting CB at the time.
Once Episode 15 of Gundam Age aired, the number of fans who are cheering for the Unknown Enemy, the Vagan, had grown exponentially. It's easy to sympathize with them as the Earth Federation left the colonists on Mars for dead, causing the said colonists to form their own nation to rival the Earth Federation.
Conversely, many fans actually cheer on Flit Asuno for trying to wipe out the Vagan race in a genocidal campaign. The fact that the Vagans themselves attack innocent civilians and earth citizens killed off much sympathy and goodwill for them. Furthermore, many named Vagans are incompetent leaders or evil for evil's sake only made things worst. That and they killed off the Ensemble Dark HorseYurin and caused Flit's Start of Darkness. In short, anyone who cheers on either the Earth Federation or the Vagans is Rooting For AN Empire.
While the Gjallarhorn of Mobile Suit Gundam: Iron-Blooded Orphans is a supposedly corrupt military organization, several officers in the organizations, such as Crank Zent, Gaelio Bauduin, Carta Issue and Julieta Juris are incorrupt, honorable and valorous soldiers who behaved like Pre-Calamity War knights, their lives are inadvertently ruined by a group of Combat PragmaticChild Soldiers. It helps that it also displays a lot of Sympathetic P.O.V. onto them rather than having Tekkadan as entirely heroic. A bit of Misaimed Fandom can be claimed here for the organization as a whole, as aside from those four characters, all we've seen are either Mook Soldiers who blindly follow orders without thinking of the morality of their actions, corrupt officers that just don't care for what they are doing and just care about their positions, or the people in charge who want to preserve the status quo regardless of how right or wrong it is. And out from the four characters, Julieta is the only one who not only stayed alive in the end but also became critical of the people who she served and realized that not everything is black or white. By the time the ending rolls in, Rustal Elion crushed Tekkadan from existence, reformed Gjallarhorn into a democratic organization and gave Mars their independence which also includes helping Kudelia abolishing the Human Debris system. Many viewers considered this the best scenario not only because it's realistic but it's unlikely for Tekkadan for win against the largest fleet in the entire system. Many also considered Rustal as a better leader than McGillis because despite using illegal weapons and black propaganda, he never attacks any civilian and never bothers to go after Kudelia regardless of her affiliation with Tekkadan which is also implied in the epilogue that he's aware of the Tekkadan survivors working for her but has no intention on going after them.
On the other hand, some viewers support McGillis Fareed due to his intent to reform Gjallarhorn despite getting his two childhood friends killed and manipulating several people along the way. Then, his Dark and Troubled Past was revealed where he was a child prostitute adopted by Izanario Fareed who also sexually abused him. It was there that McGillis had a condescending view on the people in power and desired to change Gjallarhorn on his own way which many viewers considered him as "iron-blooded orphan" like Tekkadan.
Haruhi Suzumiya seems to have rubbed some fans the wrong way — there are quite a few of them who want the Computer ClubPresident (who was the victim of Blackmail) or the Anti-SOS Brigade to succeed. In the case of the Computer Club President, it's justifiable and even Kyon has sympathy for him in-universe, because he is a victim of Haruhi's mad whims. The Anti-SOS Brigade are actually villains, however, yet back in the day they had a sizeable fanbase convinced that the Anti-SOS Brigade members deserved Kyon's friendship (and Haruhi's powers) more than the SOS Brigade and Haruhi, whom they saw as an unstable lunatic.
Given the displays of epic incompetence from the humans (namely, Meleagros and Atalantes), cheering for the Silver Tribe in Heroic Age is not hard as it seems. Mostly for them to kill those two dumbasses already.
Many fans of Jack to Mame no Ki feel that the giant Tulip should've been redeemed, seeing as he had been abused by his mother the witch Madam Hecuba and genuinely cared for Princess Margaret, and after he's finally had enough of Hecuba's abuse he kills her which breaks the spell she put on the kingdom which had turned all the servants into mice. And how do they repay Tulip?, they start attacking him and try to force him to leave when all he was really doing afterwards was slightly bullying and teasing them only because they had attacked him first, then immediately afterwards Jack starts provoking him by insulting his low intelligence much like his mother had, which leads to his death by falling from the beanstalk after Jack and his mother chop it down. While it was mentioned that he did eat people and had attempted to eat Jack before, he didn't seem to want to anymore after Hecuba's death.
La Squadra di Esecuzione, the villainous team from part 5, has a lot of supporters due to how well-written its members are. But the one who takes the cake here is Pesci, who, along with his best friend and partner Prosciutto, undergoes a LOT of Character Development despite being nothing more than a Monster of the Week in the story, going from Adorkable to increasingly vicious and determined to win. His sadness at his partner's death, which quickly turns into determination to avenge him, can make him appear sympathetic enough that you forget that he's trying to kill our heroes and kidnap an innocent girl.
Funny Valentine, the Big Bad of part 7, is motivated by extreme patriotism, his goal being to ensure the safety of his country by any means. It's not an uncommon opinion among fans that he's the true hero of Steel Ball Run, and that Johnny is a borderline Villain Protagonist in comparison. The only thing that's keeping Valentine from becoming a full Hero Antagonist is the fact that his plan, should it succeed, would only guarantee America's prosperity at the cost of turning the rest of the planet into a Crapsack World, something which doesn't make him wholly unsympathetic since he believes that if he doesn't use the Corpse Parts to achieve this, another country would do so, forcing him to be the one to act first.
Legend of Galactic Heroes is the textbook definition of this trope. Even Yang Wen-li, the military leader for the democratic government fighting the Empire, has a mancrush on Reinhard von Lohengramm, the leader of the monarchic Galactic Empire. Yang Wen-li and another wise military leader on the democratic side muse casually about how they would fight for Reinhard without a second thought if they were born in the Empire and seem to fight on behalf of a corrupt democracy with a resigned "what else can we do?" attitude. This show is also the textbook definition of Grey and Gray Morality so Reinhard isn't exactly bad...
Mazinger Z: Dr. Hell is a Large Ham who wanted to Take Over the World to force the whole humankind to bow down to him, but some fans know about his Backstory tend to see him like The Woobie (or a Woobie, Destroyer of Worlds) and actually feel sympathetic towards him, thinking it was unfair he worked so hard, scheming complex plans and strategies and crafting incredible scientific breakthroughs only to be defeated, crushed and humiliated over and over and over by a loud-mouthed, Jerkass Idiot Hero teenager with a cool Humongous Mecha. And in Mazinkaiser, it turns out one of the major reasons he wanted to rule humanity was to unite it against the rising menace of the Mykene Empire.
In Medaka Box, Big Bad Kumagawa, to the point where even the characters in story want him to beat Medaka. He has also won every popularity poll since he made his debut.
There are quite a few readers who root for the Akatsuki, and even for Sasuke during his stint as a bad guy. It doesn't help that the main character himself took his All-Loving Hero traits straight into Too Dumb to Live territory, with his doing so fueled by desperation. Though Naruto's gotten better, said fans still take Obito, Sasuke, or Madara over him.
The fans who hate Konoha and want to see it destroyed because of the Uchiha massacre being given the go-ahead, despite all the evidence pointing to the Uchiha not only bringing it upon themselves, but actually turning down the peace attempts that Hiruzen tried, especially with their It's All About Me attitude. While Konoha isn't the worst of the hidden villages when it comes to atrocities - especially given what Sunagakure did to Gaara - it's certainly not faultless either. Alternatively, some dislike it because of how Naruto was treated, even if he did ultimately end up better off than some of the other Jinchuuriki save Killer B and Yugito Nii, as if B is any indication, they were always treated with respect.
Considering that Saitama of One-Punch Man is an Invincible Hero who can defeat any opponent with one punch, looks like a particularly bland and plain cue ball, has one of the most understated backstories ever, is just a hero for fun and not because of any moral convictions or admirable ideology and whose sole goal is to get to find a Worthy Opponent, it's really not so hard to root for Boros when he shows up. First of all because, given the premise of the series, all readers know that Boros, though he has been an Invincible Villain up until now, is severely outmatched; secondly because he is a badass with an awesome design; thirdly because he is Not So Different from Saitama, being a villain who realized that Victory Is Boring and set out to conquer galaxies just so he could find someone who could put up a good match against him and, finally, because throughout the fight he goes from smug, to genuinely enjoying finally getting to use his full power against an opponent, to increasingly desperate to actually win, all the while Saitama does not even get bruised from Boros' strongest attacks.
Even fans who genuinely like Saitama and prefer him to his opponents may cheer for the villains anyway in the hopes that he'll finally get the Worthy Opponent that he's been looking for.
Garou is a lot more sympathetic than Boros and definitely invokes this, especially since most of the battles involving him against the heroes are shown from his perspective.
Pokémon has this in effect for the Team Rocket Trio Jessie, James, and Meowth. While they can succeed in some of their efforts, they are always defeated by Ash and Co. Ash has so much Plot Armor that you can expect him to win anything that's not a major tournament, and you know that he never loses to Team Rocket unless the plot demands it (remember, waaaaay back in the third episode, James' incredulous "Beaten by a Caterpie?!"). Even then it's usually by trickery rather than a battle. This goes on for so long, with even their most brilliant schemes failing, that you want them to win at least once, just to see them steal someone's Pokemon and get away with it to prove that they are still a threat. They Took a Level in Badass in the Best Wishes series, and were even promoted. Jessie, James, and Meowth are able to pull off museum heists and sneak a train out of a highly monitored subway system with little trouble, but despite this Ash still beats them when it comes down to the wire. This can leave a bad taste after watching them spend 20 episodes preparing for one big event.
The ending of Rebellion is deliberately ambiguous as to whether it's a good thing or a bad thing, but even those who acknowledge that it could be bad find it hard not to side with Akuma Homura, since she won Madoka, brought everyone back to life, and gained full control of Incubator infrastructure. Especially since the cast was already living in a Crapsack World where, even with Madoka incarnated as a goddess of hope, the incubators could potentially have been captured and enslaved her to recreate the cycle of magical girls turning into witches. Akuma Homura may have stolen Madoka's powers and altered everyone's memories, but she also created a better world and gave the entire incubator race a taste of their own medicine. It's especially cathartic for those viewers who absolutely loathed Kyubey. On the flip side, there are fans who found Homuras actions so reprehensible that they want Kyubey to defeat her, since at least he ultimately had noble intentions, as opposed to the YanderePsycho Lesbian who may be leading the universe to destruction. And quite a number of fans, even a few who hated Kyubey, have expressed the opinion that his punishmentwas far too extreme.
Record of Lodoss War has some divergences between the OVA, novels and other series but the basic plot stays the same. While at first it might look like your regular band of good guys fighting against an evil empire called Marmo who has set out to conquer all of the continent of Lodoss, it quickly shows to be much deeper. The entire land is cursed from having been the seat of the climatic battle between the Goddess of Creation and the Goddess of Destruction, and a small part of it, Marmo, is twice accursed and plagued with monsters from being the latter Godess's final resting place. Sure, the side looks stereotypically evil, being populated with a few humans and dark elves, with hordes of monsters under it's control. But their king, Beld, was a mercenary from Marmo and one of the legendary heroes who saved Lodoss by defeating the Demon King years prior. Beld claimed the demon's sword, Soulcrusher, as his reward only to be slowly influenced by its dark whisperings. His general, Lord Ashram, despite being introduced as a deadly and cold-hearted killer, proves to be a man of unfailing duty and loyalty to his king, with honor and a heart. Amidst prophecies of doom, attempted resurrections of dormant forces of destruction and a powerful witch who manipulates all factions behind the scenes out of the certitude that any side winning would upset the balance of Lodoss and cause it's doom, we get to realize that things are not so black and white. In the end, internal factions with hidden agendas and manipulative betrayers aside, the people of the Empire of Marmo really just want to get out of the terrible hell-hole that is their land and finally live in peace and safety.
In season 3 of Shakugan no Shana, many fans started supporting the Crimson Denizens instead of the Flame Hazes once war broke out between the two. Considering that the final light novel reveals Snake of the Festival Yuji and his Crimson Denizen followers not only win, but were absolutely right in believing that their dream of a paradise where Denizens and humans coexist could work and would not destroy the world, this is one of those occasions where Rooting For The Empire is supported by canon.
On the other hand, some people found Snake Yujis actions so unforgivable, especiallytowards Shana, that they side with Shana and the Flame Hazes, despite them technically being in the wrong.
Space Battleship Yamato 2199 dips into this territory, showing the Gamilas fleet battling against the Comet Empire (the Big Bads of the original series' second season), and the revelation that Earth fired first in an unprovoked attack. On the other hand, it also shows some total bastards on the Gamilas side, with one episode showing the bombardment of a rebellious planet and the strafing of refugees fleeing population centers.
Valkyria Chronicles really makes many of the Imperial characters more likable than the Gallian High Command (i.e. anyone above Varrot save for Cordelia). True, this was present in the game, but the Adaptation Expansion of Selvaria (already a likable Anti-Villain), Jaeger (an even more likable Anti-Villain), and Gregor (still as much of an asshole as ever, but compared to his Gallian counterpart Damon he's actually seen as far more competent and more genuinely deserving of respect by comparison), the Imperials look far better in terms of characterization than the Gallian Regulars, who, much like the game counterparts, treat the real heroes (Welkin Gunther and Squad 7) like crap. This is averted, however, with Prince Maximilian, who is an even more obvious Jerkass than his game counterpart.
Yatterman is better known for the three main villains than it is for the main heroes. In many ways the villains were the more focused part of the show. Heck, they (or rather, their descendants) are the heroes of the 40th anniversary special, while Yatterman are the despotic bad guys.
Dragon Ball Z features a case where most of the Z Warriors wind up taking Cell's side when Mr. Satan challenges him, as they all get irritated by his loudmouth, overbearing, braggart attitude and his constant underestimation of Cell's ability. After Cell easily dispatches him in one hit, Krillin admits to Gohan that he was rooting for Cell, and even Piccolo winds up being disappointed that Satan survived the fight.
In One Piece, a popular comic strip series shows the battles of the Marines against a guild of assassins, the Germa 66, run by Sanji's family (the Vinsmokes). While it was meant to be used as propaganda to promote the Marines, Capone Bege's right-hand man, Vito, always thought Germa was way cooler and rooted for them instead, and is thus thrilled at the opportunity to meet one of their number (Sanji).