... until Command & Conquer 3: Tiberium Wars, at which point it is getting clear that GDI have stopped being the good guys, being run mostly by corrupt politicians instead of honourable Generals, are keeping the nice and friendly Blue Zones to themselves and clearly not giving a damn about what happens to the rest of humanity forced to endure living in the Yellow Zones (the Red Zones are completely uninhabitable at this point). Then the last game clearly shows that GDI used a "Liquid Tiberium Bomb" to win in their campaign, which resulted in 25 million dead and worsening earth's state to more terrible than ever before, while also setting precedent for GDI to use Tiberium weaponry en masse, which is the last thing they would want as, due to it, they would have become no different than Nod. Also, much to the joy of Nod fans, Kane was right all along with his ideas of ascension.
Subverted for a change in Command & Conquer: Generals: The United States are mostly good, almost to a parodic degree, with lots of Type 1 Eagleland to match. They are also a bit incompetent at times. China is less good but still somewhat good, though a few of their weapons of choice are highly questionable (napalm, landmines, nukes...), and at least one of their Generals went rogue. They do end up saving the day instead of the Americans. The GLA finally are almost exclusively amoral bastards who nuke cities, douse entire populations in biotoxins, steal relief aid intended for war victims and other scummy moves, alongside employing suicide units and the like. But one cell helps the Americans, of all factions, against one of their own Generals (Dr. Thrax) because Even Evil Has Standards.
Psaro the Man Slayer subverts this partly. He hates humans because they harmed his girlfriend. But going into the arena and beating random fighters to death isn't that nice of a thing to do either. None of his underlings are ever good.
Though Psaro could be seen as sympathetic in some ways, as the death of his girlfriend drove him beyond insanity, causing him to force himself to evolve into a demonic monster who at that point doesn't even remember who his girlfriend is, and the only thing he knows in life is to destroy all humans for what they did to him, despite he doesn't even remember what that was, all he knows is that is his goal
Fire Emblem tends to play with this a lot, even with its many morally pure Lords as its protagonists.
Fire Emblem Awakening plays this straight more than any other game in the franchise; the Halidom of Ylisse worships Naga, a beautiful female dragon from an Always Lawful Good race, and is presented as pure and good while the desert theocracy Plegia is led by the Grimleal, who worships Grima, an ugly male dragon from an Always Chaotic Evil Race and is portrayed as utterly evil. An attempt is made early on to add some grey by saying Emmeryn's predecessor had made war on the Grimleal, but this is dropped, all Grimleal in the game never mention this, and are simply portrayed as bad guys who like being bad with no real motive.
Fire Emblem Fates also plays this straight for the most part, though with much more exceptions than its predecessor. The Kingdom of Hoshido is a prosperous nation that only wants to live in peace, and the Kingdom of Nohr by contrast is a Mordor-esque country with bad cropsnote You don't even learn of the crop issue in either Conquest, where you side with Nohr, or Revelations, where conquering Nohr isn't your objective. and is trying to invade Hoshido with little to no provocation. This even extends to the main rulers of those kingdoms; Queen Mikoto of Hoshido is an icon of peace, serenity, and saint like goodness in general, and King Garon of Nohr is an Obviously Evil warmongering tyrant who isn't afraid to destroy anything that gets in his way. It's rather easy to see which kingdom is supposed to be the one in the right. However, Garon is an antagonist in all routes in some form or another, it is revealed in Conquest and Revelation that the real Garon is long dead at this point, and the Garon you deal with throughout the story is actually a familiar possessing his corpse trying to carry out the plan of the real Big Bad. As a matter of fact, when he was alive, Garon was actually a pretty respectable person, going by what we're told. Garon's children on the other hand, your adopted siblings, are all portrayed sympathetically no matter which route you choose, and obviously still care for your character even when you fight against them. In addition many of their retainers, and other Nohrian units for that matter, are more or less all portrayed as decent people who are simply fighting for those they pledged their loyalty to, with their support conversations in the Conquest route giving more depth to their backstory and motivations.
Fire Emblem Warriors also has this; your team is composed of an all-star lineup of noble heroes from other worlds, and the enemy is composed of cackling bad guys motivated either by power (Oskar) or For the Evulz (the returning villains, Velezark). The only legitimately sympathetic antagonist is Darios, who ends up on the wrong end of Demonic Possession and isn't even in control of himself.
Galaxy Angel: The Transbaal Empire is good; The Val-Fasq are evil.
Subverted in Golden Sun: seemingly present during the first game, but the second game subverts it by having you play the antagonists of the first game, and having the final boss be the mentor from the first game. Despite this, the sympathetic characters from the first game have no problem switching sides immediately.
Gradius: Planet Gradius is good; Bacterion, Venom, and Salamander are evil.
But what about the Gradian government? Before the Northern Cross War that inadvertently killed nearly of the Wreekians, the Gradius government avoided contact with them because they were primitive. After the Northern Cross War, the Gradius government didn't do much at all for the poor Wreekian survivors; they only wanted to use their ESP power. This would put the Gradian government on the grey morality.
Downplayed in some of the later games. In The Legend of Zelda: Majora's Mask, the villain we are introduced to is actually just a puppet to the Man Behind the Man, and is actually just a bit mischievous, but is at heart a nice guy who just suffered from loneliness.
New Worlds Ateraan has a God of Shadows and a Goddess of Light, niftily color-coded. However, those devoted to the former would likely call Light blinding and evil, so 'good' and 'bad' are not so easily determined.
The later core games avert this though, with the evil teams having more reasonable and sympathetic motivations. The exception is Ghetsis of Team Plasma, whose villainy neighbors Cipher proportions. Cipher from Pokémon Colosseum is far more evil than anything before them and a sight more evil than anything since, up until Pokémon X and Y gave us Lysandre. Another straight example is Cyrus from Team Galactic, who seeks to destroy the current universe and build a new one in his image.
As its name suggests, Pokémon Black and White deconstructs it, with the main antagonist adhering to it then realizing in the end that no side can be truly right. It does ultimately end up as this, however: Ghetis and some of Team Plasma are evil and had their sympathetic motives be a ruse for their evil plans. This carries over to the sequel, where they don't even try to include some grey morality.
Sonic, Tails, and Knuckles are good; Doctor Eggman is evil. Shadow and Rouge border on the Grey morality, though.
Usually averted from Sonic Adventure onward. Chaos is a legendary beast who caused the destruction of a whole ancient civilization, and almost that of the modern world as well, but he's actually the protector of the Chao and guardian of the Chaos Emeralds and has no evil in his heart, he just got consumed by rage when an ancient tribe hurt the creatures he was defending in its lust for power. Gerald Robotnikprogrammed the ARK to destroy the Earth and struck a deal with Black Doom that would result in humanity being attacked and conquered by an alien race, but it's revealed that he wanted to help everyone by creating the Ultimate Life Form, and was also desperate to cure his beloved granddaughter of her illness, which forced him to accept Black Doom's help; he actually created the Eclipse Cannon to warrant that humanity had a way of stopping the Black Arms when they arrived and attacked. It's just that he went insane when said granddaughter was killed by the government's army.Solaris seeks to destroy time and space, but he's actually a good deity who went insane after being experimented on. Emerl is a robot designed as a weapon of mass destruction, but gains a kind and heroic personality through the game as a result of hanging out with Sonic and his friends and copying their traits, and keeps this one until the end, even after his programming makes him go berserk. Merlina, who is Sonic's guide and ally in Sonic and the Black Knight, is revealed to be the Big Bad at the end, but her intentions and motivations aren't evil.
Also played straight by the one-off villains in the Paper Mario and Mario & Luigi series. Okay, Count Bleck is much more sympathetic than the usual antagonist if still undeniably evil, but Fawful, Dimentio, the Shadow Queen, Cackletta, and the Shroobs are portrayed very much to the extreme end of the evil scale.
Played with in Touhou. On one hand, the series as a whole follows White and Grey Morality at worst, with copious amounts of Dark Is Not Evil and Not Always Evil, preventing the series from having any true villains. On the other hand, the interactions between youkai and humans in the games are laced with Blue and Orange Morality, with the youkai attacking and sometimes even eating humans because, well, that's what monsters do... and the humans in turn exorcising youkai, even harmless ones, because, well, they aremonsters. note It's strongly implied in supplementary material that the youkai of the setting are the natural opposites of humanity and if youkai and humans didn't distinctly define themselves by opposing each other, the youkai would cease to exist. On the third hand, the character Eiki Shiki possesses the ability to "distinctly judge anything to be Good or Evil", meaning that she sees the world in Black And White Morality. As she is the resident Judge of the Dead whom decides the ultimate fate of every deceased soul in Gensokyo, she gets a lot of mileage out of this.
Valkyria Chronicles tries to avert this trope, but ends up shooting itself in the foot because everyone on the Gallian side who isn't morally upstanding gets murdered and the only Imperials who might have been decent people also die. By the end of the game, Darcsens and non-aristocrat Gallians are good... and everyone else is dead.
In the first two WarCraft games, the Orcs are evil and the humans are good. There is some attempt to muddy the water in Warcraft II with the trolls allying with the orcs to end their persecution at the hands of humans and elves, but it's still clear who is in the right. By Warcraft III and World of Warcraft, while there are still undeniably evil forces like the Burning Legion and Scourge, it becomes less clear whether the Alliance or the Horde has the moral high ground.
Yggdra Union starts off with a princess fleeing from The Empire and raising an army to fight back against them. This later gets subverted, as the Empire isn't actually evil and is fighting for what they believe is true justice as well.
Bravely Default: Edea Lee, due to being a naive teenager who was brought up believing the lies she was told by her home country, initially believes there are only heroes and villains. Her Character Development is all about making her realize the other shades of morality in between.
The Tribunal expansion offers an aversion with the (dark) gray vs. black situation in its main quest. King Helseth vs. Almalexia, who is facing immense Sanity Slippage after losing her godhood. Helseth is not a pleasant person, but Almalexia manages to be worse...
The Bloodmoon expansion pits you against Hircine, the Daedric Prince of the Hunt, who is kidnapping the greatest warriors on Solstheim for his recurring hunt. Naturally, you must participate and defeat him.
The Knights of the Nine expansion pits you against Umaril the Unfeathered, an ancient Ayleid Sorcerer-King who has returned to get revenge on those responsible for his fall (namely, the Nine Divines). For bonus points, you actually have to purify yourself in order to wear the blessed armor required to defeat Umaril.
The Shivering Isles expansion pits you (and your Big Good supporter, Sheogorath), against Jyggalag, the Daedric Prince of Order, who returns once per Era to destroy the titular Shivering Isles, the Daedric Plane of Sheogorath. Remember that line about villains with Hidden Depths? Yeah, it very muchcomes intoplay here, but actually stopping the destruction of the realm is still pretty black and white.
The main quest pits you, The Chosen One "Dragonborn" with the immortal Aedric soul of a dragon, against Big Bad Alduin the World-Eater, the Beast of the Apocalypse. While there is an epic amount of "gray" morality surrounding you and your supporters, the actual act of defeating Alduin and saving the world is once again very black and white.
The Dawnguard DLC main quest pits you up against a group of ancient Vampire Lords who seek to create The Night That Never Ends. In a twist, you can become a Vampire Lord yourself and join their side if you so choose.
The Dragonborn DLC pits you against your Evil Counterpart, the First Dragonborn, Miraak. Defeating him and once again saving the world as we know it is fairly black and white (though you're forced to work with some pretty dark shades of gray to accomplish this).