Banjo-Kazooie: Fans like Banjo and Kazooie well enough, but Gruntilda the villain is also a very popular character, and her Evil Plan in the first game is to steal the beauty of Banjo's sister Tooty. Since Tooty was considered a Damsel Scrappy to many, more than a few fans liked the idea of Grunty getting away with it. Probably helped by the fact that, if you quit the game or get a Game Over, you're treated to a scene of her actually pulling it off and becoming a Ms. Fanservice.
Batman: Arkham City eventually reveals that the eponymous super-prison was built for the sole purpose of mass-murdering all of the inmates, including a bunch of political prisoners Strange threw in because he didn't like them. Naturally, Batman doesn't like this and the player is forced to stop it... except that the Enemy Chatter of pretty much every mook are either about how much they love murder, torture and rape, or expressions of fear of their even worse bosses. And this is in Gotham, the Trope Codifier for Cardboard Prison, with the previous game and the prequel showing that this has been going on for years, and the sequel having those same inmates turn the whole city into their playground, leaving many players concluding that this plan is the lesser of two evils given the alternative.
The alternate ending where Catwoman allows Batman to die suggests that allowing Protocol 10 to succeed would have been even worse in the long run. If Protocol 10 proceeded as planned, many inmates would still die; however, since Batman did not interfere with Protocol 10, he cannot stop the Joker at Monarch Theater due to either being dead or unable to use Talia's signal to find the Joker. The Joker would then use the Lazarus Pit, conquer Arkham City, and invade Gotham.
There's a small but vocal number of Borderlands fans who think that Handsome Jack was the hero of the series. This generally amounts to him having a sympathetic backstory, really good voice-acting, and the fact that his truest descent into insanity happened after Lilith seared the Vault symbol into his face. Jack's advocates tend to ignore the fact that he's actively trying to murder most of Pandora's population (including the decent, not-crazy civilians), he's established horrifically fascist laws in areas he controls (including execution for littering and profanity), that he regularly abuses and murders his own employees, and that he's enslaved his own daughter since she was a child, using her Siren powers to charge the Vault Key, and rendering her unable to survive without a constant flow of Eridium into her body, which eventually leads to her arranging for the Vault Hunters to kill her so she can escape the hell she's lived in.
When the MMO City of Heroes came out with their Going Rogue content the player was given the chance to start off in Praetoria -the alternate reality to Primal Earth /main reality of the game. Praetoria is embroiled in a civil war of sorts with the Empire of Emperor Cole fighting La Résistance. The general trade off was the Resistance were terrorists and the Praetorians were oppressive beyond words but at-least they were keeping the peace. It was intended as a shades of grey for morality issue... except, most players quickly found themselves on the terrorists side. Opinions varied across the community of-course, but the big sticking points were that the Praetorian government lied to its people, drugged some of them, psychically pacified the general populace, and had at least two nightmarish brainwashing facilities, one posing as a clinic the other as a jail (the clinic in particular is the stuff Nightmare Fuel is made of.). Even with murder of innocent civilians on the menu the terrorists at least offered their people a choice. This eventually took hold in-game as well, check In-Universe examples.
There are a truly astonishing number of players who believe the Brotherhood of Nod are the good guys, not GDI. While they admit Nod does some unpleasant things, they justify those by saying that Utopia Justifies the Means and that Nod is fighting fire with fire in a world where Green Rocks are killing everything, presenting themselves as humanity's only hope for survival in the long term. Nod (well, Kane) suckering a group of highly advanced aliens to land on Earth (prematurely) and then kicked them in the teeth and stole their technology probably bolstered their popularity. And then there're those that just like them for their black uniforms, laser guns and overall awesome hi-tech arsenal.
In the third game fans of Nod like to paint GDI as an undemocratic military state while saying Nod never seem to actively contradict their line that they are simply "fighting for the people". In reality, Kane frequently lies to his followers in the game about what his plans are, states he never intended to win the war against GDI, and his plan also involve bringing about the destruction of Eastern Europe and then during the Scrin invasion ordering Nod to not fight back against them while GDI continued to fight. Then in the fourth game Kane actually saves the world and gives his followers the promised power of inter-galactic travel.
Yuri's faction in Red Alert 2: Yuri's Revenge. Yuri is total monster that wants to Take Over the Worldfor his sake and his sake alone, but many fans still loved him as a villain, his faction, while overpowered and usage in multiplayer is frowned, fans still found fun to play as and were disappointed that it didn't get its own campaign.
A large number of Fallout 3 fans are adamant supporters of the Enclave, with many quite displeased that joining the Enclave was not possible in the game. This is due to the Enclave shifting from their "kill any non-pure human" agenda from Fallout 2 to using the water purifier as a means to rule the Capital Wasteland with an iron fist (mostly anyway, President Eden wants to continue with the genocide idea but Dragon-in-Chief Colonel Autumn and his men do not), along with fans who were introduced to the Fallout series in Fallout 3, so they aren't even aware of the Enclave's earlier atrocities and found them to Designated Villains. They're still ruthless fascists who consider any wastelander sub-human and will slaughter anyone who gets in their way, but since the Capital Wasteland is still such a barely functioning craphole after 200 years, it's argueable that the Enclave could finally bring order and stability. You even meet one of your father's colleagues who switches sides to help the Enclave because they actually have the technology and the means for her do finally do some real good in the wasteland, rather than desperately trying to scrape together some progress back at Rivet City. In Fallout: New Vegas there is a side quest in the game where you can bring together a band of Enclave remnants, and the rewards for doing this are some of the best items in the game. There's even a mod that not just gives the Enclave a bigger role, but also lets the Courier join them.
Speaking of Fallout: New Vegas, Caesar's Legion is a truly inexplicable example of this trope. It's repeatedly stated, and admitted by its leaders and all of its members, that the Legion ideologically endorses conquest, crucifixion and torture, rape, cannibalism, foregoing all modern technology (except certain weapons), enslavement of all women, institutionalized rape, Human Sacrifice in Caesar's name, cannibalism, genocide, genetic cleansing, totalitarian social homogeneity, and survival of the fittest. They also tolerate decimation (the practice of killing every tenth soldier in your own army in order to sustain morale through fear, something the real Roman Legion eventually deemed ineffectual) and cannibalism. It is repeatedly stated by multiple NPCs from every faction that the Legion will fail when Caesar dies, and assuming Caesar doesn't die over the course of the game he still isn't going to live much longer. The Legion's only upsides are that crime is nonexistent in Legion territory (due to the harsh penalties), that they do not tolerate drug usage (including alcohol) and that the Legion doesn't mindlessly butcher some factions in certain endings to the game. Some of this may be due to a Legion-aligned Courier receiving many perks. Getting in with the Legion provides access to a supply cache that periodically refreshes itself and a safe-house with a Luck-boosting pair of shades. (Luck being one of the hardest stats to boost on the fly.) Additionally, being opposed to the NCR, which is inadvisable for either Independent Vegas runs, allows one to freely kill and loot them, providing a Courier with as much ammo as they could ever want. But there are genuinely people who think that the Legions actions are okay because they are "building a new future".
Final Fantasy Tactics, the 1st one, featured an initial campaign against the Death Corps (or the Corpse Brigade, depending on the translation), which is run by Wiegraf, a soldier who wishes nothing more than to lead a populist revolt to unseat the corrupt nobility. We see firsthand how corrupt everyone in charge of anything is in this setting, and after the protagonist Ramza is himself on the run from the evil authorities, you're never in a position to help steer Wiegraf towards victory. Even more tragically, Wiegraf sells his soul - first figuratively, then literally - just to get by, derailing him from his original goal.
Final Fantasy Tactics Advance: A kid named Mewt has magically created a world that makes everyone he knows happier. Another kid, named Marche, controlled by the player, is trying desperately to stop him. Whether the latter is actually correct to do so is not very well explained.
The Garlean Empire in Final Fantasy XIV are one of the main antagonistic forces in the story where they invade other territories by aggressively via expansion and they either force the defeated populace to join them or die if they refuse or rebel. The empire also tries to "save" the world by slaughtering as many beastmen as possible so that they can't summon primals, aetheric god-like beings whose very existence drains the planet's life force (you later find out that not all beastmen are antagonistic or worship primals). Despite the many atrocities listed, there's a sizable amount of fans who wish that the developers can let them join the empire because they feel that said empire has better leadership, cooler toys (gunblades, uniforms, magitek based weaponry, etc), and have the power to stop the primals better than what the player character and his/her allies can do.
Final Fantasy XII has the Archiadan Empire. While you had no choice but to fight them for the plot, the Empire became ridiculously popular among the fans, in no small part due to their resemblance to the Trope Namer, right down to their own set of Darth Vader Clones known as the Judge Magisters. Judge Magister Gabranth became so much of an Ensemble Dark Horse that he eschewed Vayne as the representative villain of XII for the Dissidia series.
Worth pointing out is that, unlike most of their other examples, Square Enix portrayed the Empire in a semi-sympathetic light in a Grey-and-Grey Morality universe. While Vayne is definitely a megalomaniac, Bergan is Axe-Crazy, Gabranth murdered the King of Dalmasca and blamed it on his near-identical brother, and Ghis is a Smug Snake, they are the worst it gets. The Empire are only expanding because they believe it to be the best course of action to avoid war with their rival Rozarrian Empire, some Imperial soldiers are shown to look out for the Dalmascan citizens, and the second-in-line to the throne, Larsa, is even a guest party member at multiple points. Even the three main antagonists were working to return the reins of history back into the hands of man.
Fire Emblem: Radiant Dawn has Micaiah as the protagonist, who is arguably one of the most Base Breaking Characters in the entire series. People who find her a bland, self-righteous Mary Sue will therefore likely be rooting for Jarod to execute her, which is his goal for the entirety of Part One, along with the rest of the Dawn Brigade who are populated by bland Flat Characters who are immensely frustrating to use and level up (barring maybe Nolan).
In Fire Emblem: Three Houses, the developers apparently acknowledged this sentiment so much that they included the route — Crimson Flower — where you can literally side with the Empire and aid Emperor Edelgard in her conquest of the land, bringing down the church, and establishing a more secular, egalitarian and meritocratic society, where people are judged by their skills and efforts rather than birthright or Crests.
Gears of War: The Locust. Because they are eeeeeevil. And extremely Badass. And they have all the nice shiny monsters and freaky biological transport. And a banging hot chick for a hivequeen. It doesn't help that the COG themselves are portrayed subtly as morally questionable fascists and some of the characters are unlikable bigots. Plus the Locust themselves are only invading the surface because the planet they share with the humans was devastated by humans for centuries and they're trying to get away from the Lambent, and the COG 'won' the first war by nuking the entire surface of the planet and killing more humans than the Locusts themselves (right after the humans just ended another war).
God of War III has a fair number of people rooting for Zeus. He and the Olympians are Jerk Ass Gods, but they are at least corrupted by the evils of Pandora's Box and the order they represent is better for humanity than Kratos who has no thought beyond destroying whatever he is angry at at the moment and is willing to do anything to get his revenge even if it means destroying the world.
The Helghast are just plain more interesting - and much cooler-looking, what with the Jin Roh battle armor, comparatively more futuristic and just plain more interesting weaponry, and goggles - than their ISA counterparts. Their backstory is at least somewhat sympathetic (essentially a case of The Dog Bites Back on an unprecedented scale), and it doesn't help a bit that the human characters are either flat or actively unlikeable. Jan Templar is as bland as they come. Rico is a belligerent, Book DumbJerkass and apparently proud of these defining character traits. The girl is...wait, there was a girl, wasn't there? There has to be a girl - right? The only two characters who make any sort of impression are Helghast bigwig Scolar Visari, who gives a mean speech and is voiced by Brian Cox, and your snarky half-Helghast teammate Colonel Hakha, voiced by Sean Pertwee.
The sequel does it better, but not by much. While the ISA was made more interesting and likable, having the likes of Sev, Garza, Natko and Narville, some moron put Rico in charge, and that goes as well as one would think it would. The Helghast were given a few Kick the Dog moments to try to make them less sympathetic, but their awesomeness far overshadows that, with Visari giving a speech so awesome players are sad they can't play for the other side and the inclusion of the likes of ColonelRadec, also voiced by Sean Pertwee, who comes with less snark, but more badassery. While Killzone Mercenary lets you work with the Helghatst. It also shows there were Helghast who was willing to defect and there were genuinely evil Vektans who weren't Quislings but outright genocidal as the Helghast.
This tends to extend to the multiplayer as well. There's not much story there, of course, but many a player has groaned upon being assigned to the ISA faction, i.e. generic American soldier dudes, instead of the cooler-looking and -sounding Helghast.
Guerrilla seems to be getting the hint, due to some of the events in Shadow Fall, which portray the Helghast in a much more sympathetic light due to the devastation of their home planet in the third game. Then there's the second to last mission, which lets you play as Echo, to assassinate an ISA operative whom has jumped off the slippery slope. It should also be noted that Echo is the daughter of Hera Visari.
Organization XIII of Kingdom Hearts seems to be much, much more popular among certain parts of the fandom than the heroes, and even got their own game. They appear to have admirable goals, in that most of them believe that by completing Kingdom Hearts, they can receive hearts and be made whole once again. However, the true purpose of the Organization was to assemble Kingdom Hearts so that Xehanort could start the Keyblade War and then battle the Keys of Light so as to forge the X-Blade, and Xemnas, Xigbar, and Saïx were in on this plan by the time of II. The rest of them were just oblivious, and were given fittingly-poignant death scenes after their defeats. Except almost all of them simply reunited with their hearts and appear to be set for a return.
The Turians and their actions during the First Contact War, when the Turians decided the best way to tell the then-unknown race (Humanity) that tampering with a dormant Mass Relay was a violation of Interstellar Law, was to open-fire without warning, follow the surviving vessel back to Shanxi, then repeatedly proceed to rain down space-debris upon the settlement just to take out ground-forces and civilians. Some fans are staunch defenders of their actions, believing they were completely justified and were only upholding interstellar law. This, however, ignores the fact that Humanity wasn't a member of the Citadel and wouldn't know the laws at all. Also, supplementary materials tend to indicate that the Turians have a habit of shooting first and asking questions later as a pretext to conquer new client races and force them under the Turian Hierarchy.
Many fans believe Shepard should have stayed with Cerberus after Mass Effect 2, despite the Illusive Man being a Manipulative Bastard who was simply using Shepard for his own ends. Lampshaded by Joker in the third game, who admits that Cerberus were a lot cooler and easier to root for when they were rebels helping to save the galaxy, rather than the Indoctrinated terrorists - hampering all efforts to fight the Reapers, whilst being as Obviously Evil and Ax-Crazy as possible - they've turned into.
Saren, the villain of the first game is often the subject of this and Draco in Leather Pants from parts of the fandom. The second game reveals this even extends to being the case in-universe, where a gold statue of Saren is seen as a prized gift by wealthy criminals, while a Shadow Broker dossier reveals that there exists more than one documentary portraying Saren as a misunderstood hero.
The Geth have been saved in more games than the Quarians in Mass Effect 3 according to BioWare's own statistics, even though they were fought as enemies in every game and chose to ally with the Reapers, even if in self-defense. Much of this is probably due to Legion's popularity and that the Geth are geniuinely one of the most interesting races in the setting, while approximately three-fourths of the quarians you meet are jerkasses and the Quarian the fanbase likes the most, crew member Tali, spends at least half the game majorly on the outs with her own species.
Its worth noting that, at the time when you had the option to choose, the Geth were being attacked by the Quarians, who had put themselves in such a position that any effective counter attack would result in the functional death of their species (barring large scale cloning efforts). In essence, for those unable to save both, it was the choice between saving victims who had been established as willing to not only work with the Quarians but freely give back their home planet, and saving the people who led the attack on them. While the civilian casualties are unfortunate, it would have resulted in a genocide no matter what was done, and only one side was the aggressor.
This seems to be very much intended; while the game considers uniting Geth and Quarians in peace the best option (as evidenced by this giving the most War Assets, no one in your crew dying except Legion, who dies either way, etc.), if you cannot get this, saving the Geth is the Paragon option.
The Big BadSenator Armstrong of Metal Gear Rising has a lot of fans who actually see his overall scheme as a good thing and would happily take his side over the seemingly more sociopathic"Jack the Ripper" if it was an option. It helps that his overall plan of making everyone in America free to choose their own destinies and not be forced to "fight for money or oil or the values of others" sounds pretty good up until the "purge the weak anarchy and chaos" part, that he's one hell of a charismatic speaker, a seemingly Benevolent Boss to his henchman (if the intro to the Sam DLC is anything to go by), and a Crazy AwesomeFountain of Memes.
Basically, the fans are itching to cheer for someone, and the anemic job Blizzard has done with the setting's actual heroes so far has driven some to look elsewhere, because at least the bad guys are actually making progress.
All the Pokémon villainous teams are quite popular and get this treatment, especially from the Grunt's POVs (the leaders tend to have hidden intentions and be more malicious).
Throughout the series, fans often clamor for a means to join the Big Bad. To date, it is only possible to do this in Daggerfall and even that comes with the caveat of there being no "true" big bad (simply joining the darkest gray faction of the Grey-and-Gray Morality main quest). Game Mods which make this an option are unsurprisingly popular.
There is a fairly significant portion of the fandom who thinks Dagoth Ur was really a Well-Intentioned Extremist. These fans see him as a courageous rebel against a foreign empire who is only maligned because he was betrayed by his former friends, who then became powerful. The game itself leaves his ultimate motives ultimately unknown (though it presents ideas), somewhat encouraging this interpretation. The game design doc was originally written to allow the player to join with him, but sadly time constraints doomed that (as well as other story elements).
Almalexia from the Tribunal expansion also has her fans to the point of crossing over with Draco in Leather Pants. She has very clearly gone off the deep end without the moral ambiguity of Dagoth Ur. The fact that she returns in The Elder Scrolls Online as a leader of the Ebonhart Pact has retroactively increased her popularity in this regard.
Space Channel 5 Part 2 has the Rhythm Rogues, a group of villains who want to force the galaxy to dance for them. Their leader Purge is one of the more popular characters in the series, next to Ulala and Pudding. Rumors are going around that the real reason Part 2's getting an HD port is because of the fanbase for these guys.
Starcraft: Brood War has the United Earth Directorate. They are set up as major villains and eventually become the dominant power in the sector, forcing an Enemy Mine situation between Raynor, Fenix, Mengsk and Kerrigan to depose them out of fear they'll enslave or kill everyone regardless of race or allegiance. However... they don't. Their campaign is pretty much an eight-mission long Kick the Son of a Bitch as they spend their time fighting Mengsk and the Zerg with the mission to depose the former and enslave the latter as tools to keep peace in the sector. The major factor in this trope is that their evilness is an All There in the ManualInformed Attribute — back on Earth the UED are racist fascists who are implied to practice ethnic cleansing to curb overpopulation and genetic mutations. But aside from the implication they're infesting their own troops to use as hybrid forces, this does not come into play in the campaign. Instead their fleet leaders are shown to be honorable and reasonable people who proclaim they are there to bring peace to the sector, and given they ally with Samir Duran, the argument could easily be made the heroes could and should have allied with them instead of fighting them. There is a not inconsiderable number of fans who hope for their return in StarCraft II, even though Word of God has said it's not likely to happen any time soon.
The Heart of the Swarm campaign again has Kerrigan as the protagonist, though whether she is still a Villain Protagonist is up to interpretation. The fact that she wants to go on a Roaring Rampage of Revenge against Mengsk for leaving her to the Zerg in the first place has caused a significant portion of the fanbase to start Rooting for the Horde of Alien Locusts, because she's finally getting her vengeance and making Mengsk pay for what he's done.
Going full circle, some people in the campaign are rooting for Mengsk, seeing Kerrigan as being given the Draco in Leather Pants treatment by Blizzard and agreeing with Mengsk's declarations that she's a mass-murdering monster that needs to die for the good of the galaxy. Though he provoked her into reverting her HeelFace Turn from the first campaign, Kerrigan's actions in Heart of the Swarm completely justify Mengsk's viewpoint as she invades and infests numerous worlds and kills thousands of people for the sake of her vengeance.
In Star Wars: Battlefront and Battlefront 2 you could begin play as a Stormtrooper, but, if you racked up a high enough score without dying, could control Darth Vader or any of the awesome Sith in combat! The second game deliberately invokes this; the Clone Trooper protagonists remain sympathetic as they transition through the Jedi purge and become Vader's loyal enforcers.
You can literally root for and play a champion of The Empire in Star Wars: The Old Republic. One estimate says there are twice as many Imperial players as Republic ones on some servers. This is despite the fact that the Emperor is an omnicidal nutcase who wants to devour all life in the galaxy, the place is rife with Fantastic Racism (anyone not human or Sith pureblood is commonly referred to as "thing" or "it"), the whole damn economy is a house of cards built on military tech and slave labor, their military strategy boils down to We Have Reserves, advancement is done via Klingon Promotion (though it's gauche not to be sneaky about it for non-Sith), it's every bit as inefficient and corrupt as the Republic, and the Sith are still marking an art form of Chronic Backstabbing Disorder with everyone else ground beneath their boot heels.
It should be noted that player numbers are not a good indicator for how well-liked the Empire is in general. Light-sided or neutral Imperial characters will very much represent the Only Sane Man in the Empire working to reform it from within, and regardless of alignment the Bounty Hunter is explicitly a neutral mercenary who just happens to be working for the Empire at the moment. It's also a common opinion that the writing is of a higher quality for the Imperial plotlines, irrelevant of other consideration.
Flight duty as portrayed in Star Wars: TIE Fighter is a fairly cushy job, when compared to the matching duty in the Rebel Alliance, with rapid promotions and secret society membership benefits, both of which lead to better fighters. Indeed, TIE Fighter pilots are expected to fail against superior Alliance fighters, and since most battles take place in Empire-controlled space, recovery after ejection is highly likely. By the time you're in serious missions against rebellion forces, you're in TIE-Advanced Fighters or even TIE Defenders. Much of the time in the game you are not even fighting the rebellion, but doing what seems like legitimate and reasonable policing and military actions, such as taking down pirates, intervening in a civil war to protect the allies to the Empire and going after Imperial traitors.
Sonic the Hedgehog: The good old Dr. Eggman has a rather sizable fanbase that definitely prefer him over Sonic. Generally because Eggman's plans for world domination are actually pretty brilliant despite his temperament along with his Affably Evil personality. What helps contribute to this is how Sonic's Smug Super attitude tends to rub certain people the wrong way and just how much he tends to underestimate Eggman's competence, so many enjoy it whenever Eggman actually proves himself a credible threat despite Sonic's taunts.
Super Mario Bros.: There are but a handful of people in the Mario fanbase that prefer his Arch-EnemyBowser over the eponymous plumber. One of the main reasons is that Bowser is one of the few characters in the series with a genuine personality, particularly in the various RPG Spin offs like Paper Mario and Mario & Luigi. Meanwhile, Mario has consistently been The Everyman from day one. Also, Bowser is from all indications a loving, caring father, albeit, y'know, evil. Nintendo showed off the Switch's parental controls in a video with Bowser paying very close attention to his son's gaming habits, which many people found adorable.
Although the Orcish Horde were the main antagonists (and Villain Protagonists) in the first two Warcraft games, they were the more popular of the two factions in those days. They ended up being given a redemption storyline at the end of Warcraft 3, becoming the Trope Codifiers for the "Orc as Noble Savage" interpretation of orcs in the process. To the point that "good guy orcs" are generally called "Blizzardian Orcs" or "Warcraft style Orc".
The Horde has always had a very vocal and devout fandom, which is most commonly said to be due to the Horde being "cooler" and "more unique", thanks to being composed of playable, even noble versions of typically monstrous races, like orcs, trolls, undead and minotaurs, whereas the Alliance is a more generic human/elf/dwarf/gnome faction. They gradually became the more highly populated faction in terms of players, as Blizzard gave them a less "ugly" and more "humanlike" race, in the form of the Blood Elves in "The Burning Crusade".
Chris Metzen, the main author of WoW's storyline, is on record as saying that the Horde are the faction that he is emotionally closest to.
The official Blizzard in-house music team is blatantly Horde-focused (their name is a variant on "Level X Tauren Chieftain" and their avatar "singers" are all Horde races) and tends to glorify the Horde in lyrics — even the StarCraft II: Wings of Liberty song "Terran Up The Night" gets a dig in by insisting that the Marines would join the Horde if they lived in Azeroth.
Ever since it was announced that Garrosh Hellscream would be the final boss of Mists of Pandaria, there's been a small sect of players who have wanted to forsake the Darkspear Rebellion and side with him, either due to think he's not as bad as he's made out to be or just finding his "evil" Horde more compelling than the "good" one. Ingame players are not given an option, you have to side with the rebellion.
When the Romulan faction was originally announced a lot of fans were hoping for a proper villain faction, hewing to the TNG portrayal of the Romulan Star Empire as basically Space Fascists. Instead Cryptic chose to make the player a member of the Romulan Republic, a breakaway successor state opposed to The Remnant of the Star Empire, basing their portrayal in part on the Free Rihannsu rebellion in the Rihannsu novel series of the TOS era, and partly on the Bajoran Resistance, and undeniably the good guys (if more antiheroic than the Federation). While most players accepted the rationale that the Republic was composed of a coalition of Romulan commoners, Spock's Unificationists, and rogue military personnel opposed to the Tal'Shiar, there's still a Vocal Minority wanting a rebuilt TNG-style Star Empire.
The Vaadwaur in the Delta Rising expansion get this too, mainly because their main enemies the Kobali got a Designated Hero reaction—people have been calling their behavior towards their supposed allies (the player factions) dishonest and emotionally abusive, and their method of reproduction (necromancy) has drawn rape comparisons. Couple that with their Holier Than ThouCulture Justifies Anything attitude and the lack of ability to call them on their BS, and you can see why people might prefer the Space Nazi Vaads. Others have noted that the Kobali can't contribute as much to the alliance as the Vaads could (the Kobalis' best ship was built with Alpha Quadrant tech, whereas the Vaads have little problem taking out Voth and Borg ships), and that during the war the Vaadwaur leadership was either under Iconian Mind Control, via Puppeteer Parasites, or in the case of Gaul, just an asshole.
When the preview trailers of XCOM 2 were released, there were fans who thought ADVENT (the Ethereal-led alien coalition) more interesting and "heroic" than X-Com. A strong reason for this was due to the initial toothlessness of ADVENT's evil. Yes, they've taken over the world... but they've also given the world a great many solutions to its problems as part of that. They've provided various advanced technologies, created futuristic cities where poverty, hunger and homelessness no longer exist for any human who chooses to live inside, and they've also responsible for severely neutering if not eliminating many medical problems that plague humanity. Yes, that's right, the evil alien overlords have given us cures for things like cancer and AIDS. Even their Police State nature doesn't seem that bad when the invasive checks and interruptive scans are revealed to be a direct response to X-Com doing things like blowing up hospitals. This disintegrated once the game came out, and it was revealed that ADVENT routinely slaughters the settlements of anyone who chooses to not join their cities, and is actively engaged in genocide against humanity, abducting people and melting them into their base proteins. The success of ADVENT's in-universe Propaganda Machine makes sense, though; without that information, it's depressingly easy to spin X-Com as just a bunch of paranoid, xenophobic conspiracy theorists willing to commit acts of high-level terrorism and the Advent as truly being to humanity's benefit.
The Legend of Zelda: The Wind Waker gives recurring Big Bad Ganondorf this treatment. Unlike previous games, where he just wanted to conquer Hyrule and seize power for power's sake, this incarnation of Ganondorf is shown to be a pensive, and even remorseful, man who's been around for centuries (and a good portion of that time was spent trapped in the Sacred Realm, where he floated endlessly, without any human contact, with no hope of even death to set him free) and has a genuine Freudian Excuse: he was the king of the Gerudo, who lived in a harsh, unforgiving wasteland that inevitably killed everyone, while Hyrule was a lush, green land bursting with life and hope. Ganondorf even outright admits to "coveting" Hyrule, showing that he has some degree of self-awareness; he also goes out of his way not to kill Zelda or Link (he just knocks them unconscious to steal the pieces of the Triforce they hold) and makes some genuinely good points about how Hyrule's gods, in response to the people's prayers for protection against Ganondorf's return, came up with the solution of "drown nearly all life with rain and have a few survivors live on the mountaintops," which pushes them into downright cruelty (no explanation is ever given as to why they didn't save everyone, and indeed this is probably the least-populous world in the Zelda franchise). Granted, Ganondorf is still a maniacal warlord who begins the game by kidnapping children to find Princess Zelda and whose overall goal is to assemble the Triforce so he can make a wish upon it to burn away the Great Sea and "restore" Hyrule for the sole purpose of ruling it again, so he's definitely not good by any stretch of the imagination; it's also explicitly stated that his inability to let go of the past is a Fatal Flaw. But many fans admit to at least understanding where he's coming from at best or outright wishing he could succeed at worst (especially because said inability to move on is shared by the King of Hyrule, who performs a Heroic Sacrifice after admitting that he and Ganondorf are Not So Different).
This particular version of Ganondorf becomes Harsher in Hindsight with the release of The Legend of Zelda: Skyward Sword. That game reveals the reasoning behind why Ganondorf/Ganon, Zelda, and Link are legacy characters—it turns out that they're the ever-reborn incarnations of the Demon King Demise, the goddess Hylia, and Hylia's Champion, respectively. Demise, Hylia, and the Champion have been fighting the same pitched battle for eons in a process that will never end, so there will always be a Ganondorf, Zelda, and Link who are forced to play out their predestined roles. That's all well and good when Demise comes back as a rampaging, mindless monster like Ganon...but in this case, it feels more like Ganondorf was forced into villainy Because Destiny Says So.
In City of Heroes most of the people in the Rogue Isles, meta-human and civilian alike, love Arachnos. The meta-humans/super-villains have a free pass to do nearly anything they chose with zero moralizing as long as they don't go around wasting cities and people left and right, as for the people, well, they are very happy that with all the crazy demi-gods flying around with guns and death-rays that Arachnos prioritizes keeping them safe, relatively speaking anyway. Mean while in it's spare time Arachnos is recruiting said demi-gods into their army of doom to take over the world. This is all public knowledge by the way.
Also happened for the final phase of the Praetorian story-line at the end of the First Ward Arc. Lord Recluse ends up facing Emperor Cole to seize Praetoria as his own. It was the Card-Carrying Villain Vs The Well-Intentioned Extremist and everyone in-universe knew that at the end once Cole's psychic brainwasher is taken down and... the people were rooting for the Card-Carrying Villain straight up. Apparently people don't care about "the greater good" if you psychically possess them en-masse as part of that greater good, go figure. Regardless of intent, once Emperor Cole's smoke screen was down people were cheering on the outright super-villain over the well intentioned extremist.
In Fallout: New Vegas, Ghoul Vaquero turned mechanic Raul Alfonso Tejada is the only Companion in the core game who actually has a positive opinion on Caesar's Legion, claiming he's seen how they've "pacified" regions that were originally hellholes of violence and depravity. How he manages to reconcile his Berserk Button for people who abuse the weak, his admiration for the Legion pacifying the regions they conquer and the barbaric means by which they do so is quite a feat of mental gymnastics. But then again, none of the other companions ever had to suffer through people burn down their home when they had not enough food or water to spare, raped his sister who was out scavenging and then doing it again when he was past his prime and nearly died because of it.
Meanwhile, the only NPC who has good things to say about the Legion without being a part of the Legion's forces is a merchant from the Legion's homeland who is found in one of their camps. Naturally, his words about how peaceful and law-abiding the Legions lands are rather undercut when you can watch slaves staggering around in horrible conditions and hear the Legionaries chattering about atrocities they're performed and are looking forward to performing.