The "Crusade" in Anno1404's campaign, which is a decidedly sinister power grab under a veneer of holiness. The storyline ultimately results in the player defeating the wicked Cardinal Lucius' Corrupt Church with an institution that proves Light is Good after all.
The God from Silent Hill. She is depicted as a solar deity that will bring Paradise to humanity. Yet everything supernatural on Silent Hill, which most likely is her work, is twisted, evil and ugly, and her followers are at best insane. And, more directly, The Incubator, which has a radiant, divine appearence.
Vigoor from Ninja Gaiden. His first form looks like a stone angel
The Archangel, one of the Accursed in Riviera: The Promised Land, is 'an angel burdened with the sins of others', who tries to get revenge on the gods of Asgard.
Taken literally in The Path, where a light at the edge of the forest means that you are approaching some infinitely creepy tableau if not your character's metaphoric psychosexual death.
The Evil Empire of Xenogears is the Sacred Empire of Solaris. Despite being populated mostly by slave labor and an upper-class of unrepentant douchebags, native Solarians are mostly light-haired, most wear white clothing, their military Gears and vehicles tend to be white. Solaris itself is white. White is also a major motif of the Big Bad and his component parts. Save for a few notable exceptions, you might almost say that this game plays the trope straight.
Zanza from Xenoblade is positively angelic in appearance. He's also the go-to example of God Is Evil.
The final bosses of the House of the Dead 2 and 3 are magnificent shiny quicksilvery creatures bearing a striking contrast with the usual shambling rotten and untidy lot of the zombie army. They are still dicks though.
Solaris, the final boss of Sonic the Hedgehog (2006), is a solar deity who is literally made of light energy. He fights by shooting white laser beams at the player. Ironically, according to Solaris' character backstory, he's actually a combination of two lesser beings of different elements; Iblis, a giant lava/fire creature, and Mephiles, a bizarre shadow being.
In fact, Solaris was the original being. Iblis was the embodiment of his pure unrestrained power and Mephiles was his consciousness, which was probably shadowy and dark due to how supremely pissed off Solaris was at being experimented on.
The Bastard Of Kosigan series (fan-made Neverwinter Nights expansion) has the classic angels and demons of Christian mythology as the 'order' and 'freedom' factions of a race of precursor humans, but the 'order' faction (who are definitely rather nasty, going directly to deadly force whenever anyone says 'no' to them) eventually won their war for the hearts and minds of ordinary humans and killed all the 'chaos' faction (except for two 'demons', one of whom is revealed to have been St. John and the other is your character's deceased mother, who stole Archangel Gabriel's (the leader of the 'order' faction) sword.)
The H-Game Monster Girl Quest has one in the Goddess Ilias who ends up being the Big Bad who caused the Slaughter of Remina, and, by the end of chapter 2, attempts to eradicate all of humanity on top of trying to kill all of the monsters, which she had been trying to do from the beginning. She also looks like a pure angel.
One of the major plot points in Tales of Symphonia. The major villain, Mithos, is a Fallen Hero, and his main form of attack carries over into his villainous style. Appearing as a bishonen angel with wings of multifaceted crystal, he uses mainly Light based attacks, and has a very specific vulnerability. What is it? Why, darkness! In fact, all the angels except Kratos and Yuan have that weakness.
Only two of the Summon Spirit boss fights result in a Game Over when you lose, one being the humanity-hating Volt, and the other is the Luna and Aska battle, and Luna and Aska are the Summon Spirits of Light. They're the last Summon Spirits to form a pact with, and since Kratos is on the previous floor, there's no opportunity to leave and level up. So a Game Over is the only logical end to a lost battle.
The final form of Duke, the last boss of Tales of Vesperia, has a mystic arte that ends with a move that looks like Estelle's Sacred Penance, called Brave Vesperia, a compilation of your seven party members' Mystic Artes. Shame the PS3 version of the game doesn't add Flynn's and Patty's Mystic Artes. However, despite his shining appearance, Duke is not actually light-elemental. And despite being the Final Boss, he really is good in the end.
Regardless of their leader's alleged Omniscient Morality License, Celestia in Disgaea qualifies as this. Though not evil, they are people capable of being very wrong while also being very sure they're right, and aren't above Fantastic Racism towards demons and humans. We do know that Lamington and Flonne aren't as apeshit about order as Vulcanus, but the rest...
Actually in this sense it would seem that Lamington was usurped by the ambitious Vulcanus (despite him having no chance), and the rest of the angels merely followed orders. Lamington never actually does anything offensive besides dealing with Vulcanus and Flonne, however Flonne is dealt with by their laws and in the good ending returns as a fallen angel rather than being turned into a flower. Flonne seems to be ruled more by The Power of Love and the Rule of Cool than anything else. She has no prejudices (and in fact states as much early in the game) and no real desires beyond living a happy life and bringing love to those around her.
The spell "Holy" in many installments of the series is a beam or explosion of divine light that burns the target from the astral plane, and is usually earned late in the game. Plenty of adversaries (mostly evil ones, who might even belong to a Corrupt Church) use it on you with impunity.
The GBA remake of Final Fantasy II has the Light Emperor. Specifically he is the "good" side of the Emperor's soul split from the "evil" side in Pandemonium. He tries to take over heaven, and succeeds completely, becoming master of heaven and hell before you even get there. He's still a tosser though.
Final Fantasy III had the good-guy Warriors of Darkness in its backstory, fighting the "Flood of Light" that threatened to burn away all of creation and was every bit as evil and dangerous as the Cloud of Darkness that the player-controlled Warriors of Light are now up against.
Holy was supposed to save the Planet from Meteor. It was summoned so late, though, that its clash with the Black Magic spell was actually devastating what it was meant to protect, until the Lifestream surged up and helped it destroy Meteor. Even then, Bugenhagen theorized that Holy, a spell that obliterates that which is harmful to the Planet, could have very well destroyed mankind as well, if it judged humans to be harmful. The game's ending was deliberately ambiguous about whether this had in fact happened (with the ending's only post-Holy scene depicting solely non-human characters), but the spinoffs and sequel movie made it clear that humanity survived.
The Church of Yevon, which (initially) seemed like a good organization, if a bit bigoted, bringing hope and order to Spira. Then the Maesters showed their true colors...
There's also Yunalesca, a stunningly beautiful woman with long white hair, fair skin and silver clothes. She was the first summoner to defeat Sin and waits in Zanarkand to await summoners that complete their pilgrimage. And if they don't do what she says, she has a horrific One-Winged Angel.
The gods Alexander (light) and Odin (darkness) are in constant opposition. Every few hundred years they break free from where ever they are to fight each other in a "Ragnarok", in an attempt to destroy each other and mowing down anyone in their paths. Showing that Dark Is Not Evil, Odin is the more magnanimous of the two as he, beseeched by a servant who had repeatedly defied Odin's orders, saves the life of an Empress who was shot with a holy beam meant for him.
Beastmen summoners are capable of using the Light-based Avatar Carbuncle for their Astral Flow ability, generally with more disastrous results than the normal elemental Avatars. Also you learn in the Chains of Promathia expansion that the Beastmen are actually the creations of the Dawn/Light Goddess Altana, while the playable character races are the creations of the Dusk/Dark God Promathia. Basically it's the playable forces of Darkness whaling on the creatures of Light who are just trying to live in peace and harmony with each other.
Light elementals are just as pernicious once roused as their dark brethren, and by the same token, a dark elemental is just as peaceful as a light when left alone.
Ultima, the strongest of the main twelve Espers, is a personification of this trope. Her element of choice is light. She has a beautiful, angelic appearance (complete with platinum blonde hair and a feathery dress) - and is a very tough, powerful boss who uses magick fields to weaken the player, wields very strong Holy magick, and can inflict Reverse on a character and use Renew to KO them. She also led the rebellion of the Espers against the gods. Though you can get her to be on your side if you beat her...
Final Fantasy Tactics also relies heavily on this trope, as most of the main villains could fit this category in a way or another. Pretty much all of the Shrine Knights and the high-ranking members of the Church of Glabados fit this trope well. The last boss in particular is the reincarnation of a false saint with a whole corrupted religion revolving around him/her/it.
In Makai Toshi SaGa, the final Boss, the Creator, is not only light, but is God, and attacks with what is essentially the light of God.
In Chrono Cross, light (white) is the elemental attribute of the hero, but also of many villains, often among the most powerful, including the final boss. Most of the strong white innate bosses you fight are placed in the time where you will be in Lynx's body. Lynx's innate is black, and white elements deal extra damage to black innate. Hope you got some Diminish.
Fortinbras, the Big Bad from Onimusha: Dawn of Dreams comes to mind. All of his attacks are light-based, and he even walks onto the battlefield wearing all white. He specifically refers to himself as the 'God of Light'. Conversely, the main character is sometimes known as the 'Oni of the Ash'.
Combining "value-neutral elements" with "too much of a good thing" gives us the Sun Rune in Suikoden V. Properly sealed away, it provided light and perpetual fertility for the Queendom of Felena. Like all True Runes, it has a will of its own, however, and if taken into someone's body, it seems to slowly twist them into an imperial tyrant. Ultimately, it may be one more case of that universe's take on Order Versus Chaos. To be fair, the Sun Rune, Dawn rune, and Dusk Rune come as a set, and it is explained in the course of the game that the Sun Rune will not corrupt its bearer if said bearer also possesses the other two runes. Since a major plot point is that one of the runes has been stolen, we never actually see this...
Deliberately invoked throughout Devil May Cry 4. The villains are a Corrupt Church. Their signature soldiers are the beautiful Angelo living armors, crafted with a glorious mixture of angelic and demonic features and deliberately created as "angels." By contrast, main character Nero's sinister Evil Hand turns out to be a powerful force for good. Interestingly, the villain's raison d'etre, using demonic energy to kill all the demons in the world, isn't necessarily a bad one, but in the third act of the game, it's pretty obviously shown that Extremism has taken root, so they've become da bad dudes.
Also the "Fallen" enemy in the third game. The figures appear angelic...until they spread their wings and reveal a monstrous face on their torsos.
Beowulf (no relation to the hero) from the third game too. A light-elemental demon, complete with pseudo-Tron Lines, with a desire to see every blood relation of Sparda dead. He is a tough nut to crack too.
The angels in the Diablo franchise are portrayed as being manipulative and having no feelings for humans beyond using them to fight the demons. The necromancers believe that although the demons winning would lead to an eternity of torture for mankind, the angels winning would lead to domination and mental stagnation, and so the balance must be maintained. The main exception to this rule is the archangel Tyrael, who started out spiteful to humans but grew to appreciate them.
And Auriel and a few others, but they certainly don't align with High Heavens policy. In fact, whereas the demons just want to enslave mankind, the angels in general and Imperius and Malthael in particular tried to destroy the mortal world because they deemed it a taint on creation. Also, humankind used to be a lot more magically powerful in the past, until the antimagic effects of the Worldstone (thanks to renegade angel, Inarius) took hold. Then when a group of humans rediscovered their ancient power and managed to resist an angelic invasion intent on destroying the mortal world, the only lasting impact was that the mortal plane was allowed to continue to exist—thanks to Tyrael convincing the Angiris Council that people do have feelings—albeit without their powers, with the Worldstone still there and the plane itself only protected from extraplanar influence by a brittle pact between the Council and Mephisto, who naturally circumvented the pact and proceeded to do the things demons do in Diablo while the angels stand by and watch. This plot twist is found in the third book of the Sin War series, and is rather scary in a Cthulhu sort of way. These are angels who almost destroyed our universe, then were only prevented from finishing the job by democratic vote, then took away humankind's power and allowed the mortal world to be overrun by demons and people to get killed in a lot of creative ways, just to see if humankind would eventually grow up to fight off the demons by themselves and join their ranks—or presumably face the judgement anyway. Think about that when you get killed by Blessed Hammer in Pv PAGAIN.
Well, the brain behind the Scarlet Crusade is Balnazzar, a Dread Lord working on behalf of the Burning Legion. And then there is the highlord of the Crusade, who is an undead himself.
Another example of non-good paladins are the blood elven paladin (AKA the Blood Knights), who derive their powers from a kidnapped being made of pure light.
Although later advances of the plot of Burning Crusade have seen the blood elves' former leader, Kael'thas, who was then in league with the Big Bad, forcibly take the captured Naaru from his people and use it for his own nefarious purposes. The leader of the Blood Knights later pledged her warriors to stopping their former leader and were blessed with the Light by another Naaru.
Said Crusade may have taken inspiration from Prince Arthas, who slaughtered a town in the name of the Light. Granted, said town was already infected with a virus to turn the villagers into zombies, but praying for a cure or something might've been a better idea. And it only gets worse from there until he claims Frostmourne at the cost of his soul and turns evil.
There's also the val'kyr, servants of the Lich King, who look like stereotypical angels, but are, according to official description, "fearsome creatures made of pure nightmare".
Playing a Paladin or Priest can go in this direction, with a slight variation to a holy spec (which means normally healing) and the right equipment they become devastating powers. The Priest is in a holy spec in the early levels far stronger in offensive. But in the higher level this changed with the new skill trees in patch 3.0 for the Wrath extension: the Shockadin (Paladin dealing damage with Holy Shock) is pretty dead and the Priest version (the Smiter) lacks in raid support compared to the Shadow Priest counterpart.
The Shadow spec for the Priest class. You may follow the Light and have the power to heal others, but your real talent lies in Mind Rape.
Some skeleton Paladins in Icecrown have their own interesting variation on the Light created from Void/Shadow Energies.
And there's arguably the Burning Legion itself, insofar that they are frequently associated with destroying flames and were led by a corrupted titan. Those flames are mixed with their Casting a Shadow powers making them both this and Dark Is Evil.
The ultra-bigoted General Ripper Grand Marshal Garithos has Holy Light and Holy Shield.
The Angelus displays this well in The Darkness II, albeit mostly through Flavor Text found in certain holy (and not so holy) relics. Bound the souls of a hundred children to her purpose, possessed a woman to slaughter a village, roasted the unkillable Cain alive when he came to her to help with his atonement, and managed to completely burn the soul of the one Brotherhood member to save the world from destruction, into absolute nothingness. And just for a kicker, proves itself even more underhanded than The Darkness itself, tricking Jackie into sending himself to hell to help Jenny, only to leave him in hell so she won't have to actually fight The Darkness herself
Fire Emblem: Radiant Dawn uses this as well as Order Versus Chaos. The villains of the game are the Begnion Senate, which is obviously modeled after the medieval Catholic Church. All of the senators are the Bishop class and use light magic. One of them uses corrupted light magic. Ashera, Goddess of Order, is the final boss, as she wishes to punish the world with the light of judgment, and our heroes team up with the (very nice) Goddess of Chaos to stop her. The Order Versus Chaos page explains this all very nicely.
The entire series uses both this and Dark Is Not Evil, because classes specializing in healing or light magic are quite frequent in the enemy armies, including among their often flatly evil bosses, and classes specializing in dark magic can be good. (In fact, in every chapter of the first game's second half, expect at least one Cleric with a Reserve Wand.) However, there's still a tendency towards the nastiest magical characters being hideous and/or using dark magic, and the reverse for the good side.
It's explained that light magic draws its power from faith, and that dark magic draws its power from knowledge, creating a sort of religion-science dichotomy between the two. If you'll notice, even the most evil of Bishops (like Kenneth or Riev) have absolute faith in the villains, and most of the series' dark magic users (at least since Sword of Seals) have been extremely intelligent bookworms, regardless of their alignment to good or evil. The series tries to avoid the subject of religion for the most part, but Kenneth laughs at the idea of gods, cementing the idea that object of a light magic user's faith doesn't need to be divine.
In Path of Radiance, you have to take down a corrupt bishop who stole a heron. He uses one of the most powerful light spells in the game. Said character also happens to have an army of other light magicians with him.
If you get betrayed ANYWHERE in the series, 2:1 odds are that it was by a bishop, cleric, paladin, light magician... you get the point.
The Big Bad of Sam And Max Season 1, Hugh Bliss, is a self-help guru who wears all-white, is a kindly old man/aging blissed-out hippy, and uses rainbow-colored magic. He's also building a giant mind-control beam on the moon designed to make everyone on Earth as happy as he is. Turns out, he's a sentient colony of space-faring bacteria that feeds on human happiness.
Best part about that? You get to stop the Big Bad, which necessarily means turning the world into a Crapsack World again. And the only way to "cure" the hypnotized happy people is by punching them in the face. Max gleefully spends the credits doing so.
Well, actually, defeating the Big Bad changes the mind-control beam. Instead of everyone acting oh-so-very happy and cheerful and kind, everyone on the planet is acting like Max. So, punching everyone in the face...is definitely necessary.
In Planescape: Torment, Trias the angelic deva desires nothing more than to aid the Heavens in recognizing and combating the threat posed by the fiendish Lower Planes... so he decided to get the Lower Planes to wage bloody war on them. After all, they're only fiends, they deserve what they get...and the Upper Planes deserve the pain they get for not treating evil as a true threat, and casting him out...
Castlevania has the Amalaric (or Goth Sniper), a minor enemy that looks like a white torso with wings and a bow and is described as a fallen angel. While in Symphony of the Night and Dawn of Sorrow he's quite a pushover, in Portrait of Ruin he gets a boost on his attack power, becomes resistant to Holy damage, and gains a new attack that shoots arrows in ALL directions.
Castlevania: Order of Ecclesia introduces the White Fomor, a twelve-foot-tall hovering goat-headed man-thing who shot balls of light at you, and he "mocks God with his blasphemous chanting."
Speaking of Order of Ecclesia, Ecclesia's true purpose is to fulfill mankind's "greatest wish": The return of Dracula.
In the online Flash RPG AdventureQuest, Brilhado are humanoids with dark purple wings with red tips. Books in the Temple of Hope say people once called them Angels but are really Greater Light Demons. AQ Demons are not satanic, but are creatures from the elemental realms. The Brilhado are Greater Demons because they are even seen as demons in the elemental realms. Most of them work for N.O.V.A.
Subverted by Diviara, though a Brilhado, is a Necromancer, who wears black robes, though his weapon, Duality switches between Light and Darkness elements. He is a general of N.O.V.A. but after his brother's death joins you.
Played straight by Mori Motonari in Sengoku Basara who claims to be a "Child of the Sun", and is a Light-elemental character (which means he can break enemy defences). Except that he's The Chessmaster and a sadistic Jerkass who could care less about his soldiers' welfare so long as they just do as he commands, treating them like disposable pawns. Exemplified with the fact that in-game, he can actually attack his own allies, a trait shared only with psychopath Akechi Mitsuhide. This is lampshaded by Oichi, the series' poster girl of Dark Is Not Evil, in the spin-off Sengoku Basara X who goes on to say that his "light is a lie" if they ever face each other.
Imagawa Yoshimoto, though not evil, is a Dirty Coward whose only connection to Light is merely his love for disco and as such summons light shows for attacks.
In general, Sengoku Basara seems prone to give the "Light" element to unsympathetic characters, like Otomo Sorin and Honganji Kennyo. There are still good examples, though (like Ieyasu and Nagamasa.)
In Grandia II the Pope of the popular religion turns out to be helping to revive Valmar (the game's Satan analogue) because contrary to the world's standard mythology, Granas (the "God"/Crystal Dragon Jesus of said popular religion) lost the ancient "Battle Between Good and Evil". Said Pope also seems to actually be much more evil than Valmar, and sought to revive the "devil" to steal its power and make himself into a replacement for the long-dead Granas. Mareg's religion doesn't believe in complete evil or good (much to the disdain to one character) and is proved correct when the "real" history of the gods is shown to the heroes.
In the Shin Megami Tensei games there are usually the alignment choices of Law (Light), Chaos (Dark), and Neutral (Whatever) (each having their own advantages and flaws). Law's flaws are that the rules are too strict and harsh, and that anybody who doesn't obey the rules must be eliminated. In fact the only reason the Chaos alignment exists is to stop the Law alignment's tyrannical reign.
Some Shin Megami Tensei games additionally have a Light/Neutral/Dark alignment axis. This refers to the mythological reputation of the entity as something to be reviled or revered, and has no bearing on its actual morality — the below-mentioned YHWH and his higher-ranking Angels are as far along the Light axis as you can get, and are petty, self-centered megalomaniacs.
Especially seen in Shin Megami Tensei II and Nocturne where YHWH is the true ending's final boss in the former and a total douchebag in the latter.
Light as an elemental spell. In the Persona subseries, Light's main form of offense is insta-kill spells, identical to Dark except for their element. Sometimes seemingly Light-oriented personae will learn both Light and Dark spells. Whether or not these spells are effective, Light as an element can be pretty dang cruel.
Nyarlathotep, the Crawling Chaos from Persona 2: Innocent Sin, has Light-based spells when he poses as both Hitler and his Persona, as well as when he takes over Jun's/Joker's body.
In Shin Megami Tensei III: Nocturne, there are a couple of incredibly malevolent Light spells. Amaterasu's Godly Light instantly destroys 80% HP of everyone in your party who does not null Light. Kagutsuchi's Vast Light and Infinite Light are both monstrously powerful Almighty moves, meaning you can't null them and they will hurt if they don't outright vaporize everyone. Radiance can obliterate entire parties with one casting. Thunderclap and Holy Wrath can mow everyone's HP to half. Metatron's Fire of Sinai not only deals random Almighty damage, but can also extend to insta-kills. So yes, pretty dang cruel.
Mitra's Light of Order is a One-Hit Kill to a random demon in your active party. Ironically, Mitra's alignment is Dark-Chaos.
Metatron's Judgment Light insta-kills with 80% efficiency, for those not weak to Light.
Also plot-wise, Zelenin's transformation into an angel practically turns her into a walking demon-slaughtering human-brainwashing machine. Who enjoys the whole thing. It is creepy even if you're going for the Law ending...
In the Kirby Super Star Ultra subgame Meta Knightmare Ultra, Meta Knight ends up fighting against a Light Is Not Good Evil Counterpart. Playing the Blood KnightAnti-Hero in this game, he wishes to Nova that he could fight the greatest warrior in the galaxy to improve his skills. It turns out it's a being that looks like an angelic version of Meta Knight and was sealed away because its sheer power presented a danger to the galaxy.
Played straight again in Kirby Triple Deluxe, with the main antagonist Queen Sectonia being associated with light and creation.
All of the Totema bosses of Final Fantasy Tactics Advance use are healed by Holy, and some use it too. One of the game's most powerful swords does Holy-elemental damage, much to the dismay of many players who went into the final battle with it equipped.
Phantasy Star IV has this as a major theme toward the end of the game. The Great Light, the creator god of Algo, is not shown to be good, just not straight-up evil. The main character, Chaz, has a moral objection to the expectation that he and his companions should do the Great Light's bidding, being that the Great Light itself abandoned the solar system ages ago, and that doing so would make them no different from Zio, the cult leader/evil wizard who killed his mentor figure. More directly, though, the elemental Light creatures are few in number, live in idyllic, magical crystal castles, are immortal figures made of glowing fire. De-Vars, Sa-Lews, and Re-Faze embody Strength, Courage, and Anger respectively, and while they're all pleased that that the heroes triumph over them, they do make a point of trying to crush them in order to make sure they're worthy of the task of saving the universe. Re-Faze in particular is willing to isolate, trick, traumatize, and insult Chaz in order to test his mettle. In the end, only good can truly triumph over evil, and good can only exist in the human heart.
Also, all the Light elemental attacks are pretty badass. In PSIV, if it looks like a laser, you can expect it to do some pretty hefty damage. In a couple of boss fights, the wussy second-level Githu technique (it's basically a yellow laser that goes bzweeoon) does more damage than most melee attacks.
A similar theme occurs in Phantasy Star Universe, only taking the light from aloof to outright evil. The Ancients, who have represented the light element, and directly opposed to the darkness of SEED are eventually revealed to have been, with some exceptions, a race of tremendous jerkasses lead by a man so incredibly twisted it's implied he raped and killed one of his (many) wives who view current humans as nothing more than vessels for their resurrection. To illustrate the point further, this leader styles himself as "the Sun King".
The sequel, Bomberman 64: The Second Attack provides three examples to this trope. First there's the boss, Zoniha, whose title is "The Purifying Light" and attacks with, you guessed it, light based attacks. Though her case is arguable since she was brainwashed by the Big Bad to do evil deeds. The second case is the penultimate boss who is literally a goddess of light who decides to pass judgment on Bomberman for refusing to cooperate with her. The final example is the final boss, the angel of light and darkness, who seems to focus more on light attacks than dark ones.
Copy X from Mega Man Zero and Lumine from Mega Man X 8, which take on angelic forms during their boss battles. The Classic series has Bright Man and Flash Man who also have light-based powers, and they're antagonists (though Bright Man is one of Dr. Cossack's creations, who attacked Mega Man due to Wily's manipulations).
There's also the light-themed Mavericks from the X series, such as Sting Chameleon, Neon Tiger, and Optic Sunflower. EspeciallyOptic Sunflower.
Destroyman in No More Heroes appears to be a superhero and claims to fight with honour...but it's not hard to see that he's one of the most dirty fighting, Ax-Crazy assassins that Travis has to fight.
The Angels in Bayonetta, which are best described as "grotesque monstrosities with marble-colored skin, stereotypical Greekish clothing, wings, and halos."
More extreme is the Big Bad, Father Balder. The last of the Lumen Sages, he orchestrated the genocide of both them and the Umbra Witches, killed Luca's father, is the one commanding the angels, and does not seem to care for his daughter beyond being a tool for the awakening of Jubileus, who he intends to use to destroy the current universe so that a prettier one can be created.
Jak's own Light form comes complete with a set of angelic wings. While its powers are mostly based on defense rather than offense, it still enables Jak to wreak havoc, for example by using Flash Freeze and then shooting everything in sight.
Arguably The Legend of Zelda: Twilight Princess, where the Twilight realm would have stayed peaceful if not for Ganondorf, a light being. Ganondorf is the big bad of the whole series, and he was one of the three people blessed with a piece of the Triforce. He also fights with a sword of Light in Twilight Princess
Ghirahim in Skyward Sword has a predominantly "white" look, but he's clearly a villain. The whiteness gradually "molts" off, though, revealing the dark demon underneath.
Very little is known about the Fierce Deity from Majora's Mask, but when you get his mask, you get the message "Could its dark power be as bad as Majora?"
The Light school of magic in Dawn Of Magic deals radiation damage.
Dominions 3 has it's fair share of evil Light nations. Take for example Marignon, a nation led by an inquisition that went too far in their search of heresy that they made a pact with demons and started practicing blood magic to increase the effectiveness of the inquisition. But then, there are no "good" nations in Dominions.
Want to permanently brainwash enemy civilians into zealot loyal to your cause? (Disclaimer: The process is far from perfect, only some will be properly converted, others will be driven irrevocably insane or will simply die.) There's an astral spell for that. Want to curse somebody for the rest of their lives? There's an astral spell for that, too. Want to cause a province-wide epidemic of bad luck? Astral magic. Want to paint a unremovable bullseye on somebody that will make them a target for any passing Eldritch Abomination? Yep, astral magic. Want to send an Eldritch Abomination to wreck havoc on a distant province? You're going to need astral magic. Want to forge an Artifact of Doom? A lot of them require skill in astral magic. Want to taint the source of magic itself, so that only Blood Magic is safe to use? Hope you've got at least six levels in the astral path.
Taki's, Siegfried's, and Cassandra's endings in Soul Calibur IV touch upon the fact that the titular spirit sword can easily be just as dangerous and manipulative as its darker counterpart and precursor, Soul Edge.
This is confirmed in Soul Calibur V'' with the appearance of Elysium, Soul Calibur's personification in the same vein as Soul Edge's Inferno. Soul Calibur wants order, and doesn't care how it gets it.
Jin Kisaragi of BlazBlue is very handsome, has blonde hair, wears brightly colored clothing, and is celebrated as the Hero of Ikaruga, a war which took place some years before the game. He's also an enormous Jerkass who possesses very few redeeming qualities, is easily angered, and who's Yandere for his brother, Ragna. However, by the end of Continuum Shift, it has appeared that he's pulled a Heel-Face Turn, and may be slightly closer to Light Is Good.
On the other hand, Jin's girlfriend, Tsubaki Yayoi, uses the Armagus Izayoi, a light-based weapon. Except that rather than simple light manipulation, this is some sort of Evil Weapon that steals light from other people, causing the user to go blind. Tsubaki thus far managed to avert this trope... until she got Mind Raped by Hazama, turning into a Green-Eyed Monster bent to kill Noel for a selfish desire, playing the trope straight.
The Izayoi's reputation as a very nasty Sealed Weapon has spread far and wide, and everyone in the know who isn't Hazama or Relius voices their objections to her wielding it. In her Story mode, Jin is exasperated that she would wield it, and Hakumen's Story mode conversation with Jin is a request to save her both from Terumi's machinations and from it. Ragna, after defeating her in Arcade mode, tells her to get rid of it immediately, and if her combat quotes are any indication, Makoto's not fond of it either.
When we first see Mu-12, she descends from the Cauldron bathed in a bright light, lending her an almost angelic appearance. Also, most of her attacks are light-based to some extent. She's also known as Kusanagi, the sword that slays gods, and is brainwashed by the Big Bad.
A major theme in Disgaea, along with Dark Is Not Evil. The villain in the first game is an archangel who manipulates humans to start a war with the demons and attempts to ascend into godhood in order to bring about absolute peace by forcing all angels, humans and demons to do as he commands. Despite what they themselves believe, neither demons or angels are absolute good or evil, but both are capable of actions of either morality.
The Elyos in Aion. They look angelic, and tend to be comparatively more gentle than the Asmodians. They're also arrogant, self-absorbed, and just as dedicated to the petty and vindictive war against the Asmodians as the Asmodians are to the war against them.
Despite the first game taking a straight "light is good, and dark is bad" angle, most of the Kingdom Hearts series affirms that light and darkness are simply sources of power. What you do with them is completely up to you, and later games introduce light-wielding villains.
Not to mention one of the arc phrases of the first game: "The closer you are to the light, the greater your shadow becomes."
Furcadia's "Light Primes" are generally not nice. For example, Viveravus, the good god of colors and the twilight, literally tore Tallus to itsy bitsy pieces with his own two hands in public, at Mycrofts of all places, regardless of what the game cannon says. Tallus did not even fight back, he just kept trying to defend himself against an unprovoked attack against an angry drunk god. This happened in front of a bar full of horrified mortals. He also threatened to attack said mortals. Also, meeting many of the light primes in person can be a shock most of them are jerks. Aristaya, the goddess of good dreams, is a regal ice queen, M'rill the sun goddess is full of herself and will rob you blind, and Chim will challenge you to games at which you will almost certainly always loose. The rest of the gods can be even worse...
Throughout The Legend of Dragoon, historians, priests and various worshipers speak of the Moon Child, a saviour reincarnated once every one hundred and eight years to bring holy bliss and purity to the world: however, for the past eleven thousand years, the Moon Child has been killed by a nightmarish demon known only as "The Black Monster." Well, with all the cliches at work in this game, you'd expect that your ultimate goal in the last disc is to kill the Black Monster and help the latest incarnation of the Moon Child purify the world, right? Wrong. It turns out that the Moon Child is really the misplaced soul of the Virage Embryo, the God of Destruction. And once the two are reunited, the world will indeed be purified... by being completely destroyed.
The Legend of Dragoon takes it even further: Each character is associated with one of 7 elements. Your first archer, Shana, turns out to be the Moon Child. What element do the archers represent? Light.
Seiken Densetsu 3 features 8 elemental God-Beasts of destruction who had to be banished before the world could be created. During the course of the game, they all get revived and it's your job to bury them again. Light, like any other element, has its own God-Beast: Lightgazer, an eternally-staring floating eye occupying a ruined "City of Light".
For a Dark Is Not Evil counterpart to this, the game also features 8 elemental spirits who helped you out. Shade, the slightly scary-looking spirit of darkness, is just as friendly and helpful as any of the others.
Tenshi of the Touhou series is the Big Bad of Scarlet Weather Rhapsody. She's a Celestial, essentially the series' version of an angel. She also caused the various incidents in that game, from causing tons of weather disturbances to threatening to unleash a massive earthquake. Why? Because she found heaven boring and so she decided to endanger all of Gensokyo For the Evulz. Light is a Jerkass.
Reimu, the amazing flying miko and main heroine of the series, is also an unrepentant jerkass at times (see the "Reimu is a bitch" meme), and the newer miko player character, Sanae, has wandered into She Who Fights Monsters territory.
Unidentified Fantastic Object had at least two holy characters (Shou Toramaru, avatar of the god Bishamonten, and Byakuren Hijiri, a Bhuddist nun turned magician youkai who was responsible for Shou becoming Bishamonten's avatar) who favor youkai over humans and oppose the heroines.
Well, more like is opposed by the heroines. She just gets out of an eternity of imprisonment for no reason and suddenly lasers and amulets everywhere!
EVE Online has the Amarr Empire as one of the main factions in the game. They are a pure and devoutly religious people who protect the galaxy from evil with their beautiful golden spaceships. However, these beautiful spaceships are enormous monstrosities like the 'Apocalypse' and 'Armageddon' battleships with laser cannons that are arguably the most powerful weapons in the game that can turn most opponents into dust in minutes. And how do they protect the galaxy from evil? By conquering as much of it as they can, enslaving other races that oppose them and claiming divine right to do whatever they feel like to anyone they feel like as servants of a higher power. The only thing that stopped them cold was a far more advanced and powerful race which they tried to claim as their property. Since then, they have put their plans for purging the galaxy of evil on hold.
Nova Praetoria by far the brightest, shiniest zone in all of City of Heroes. There's a bright Gold on White Motif, all of the civilians are happy, statues of superheroes dot the landscape, and one of the first missions involves picking flowers. This is the Evil Mirror Universe version of Paragon City.
With the new side switching system, now even the brightest, most light oriented Empathy/Energy Blast Defender can be a villain!
2 examples from the Daedra in The Elder Scrolls IV: Oblivion. The Aurorans in Knights of the Nine are the servants of Meridia, the Daedra Lord of life and energy; in the game they have allied with one of her servants, Umaril, who seeks the downfall of The Nine Divines. The Golden Saints (Aureal in their own language) are employed as enforcers by Sheogorath the Madgod; while they aren't outright evil, they frown upon mortals as unworthy and are a lot less sympathetic than their counterparts, the Dark Seducers.
That said, the man who opposed the Aurorans and Umaril was Pelinal Whitestrake who is as insanely genocidal as Umaril was.
The Thalmor soldiers in The Elder Scrolls V: Skyrim wear the standard golden Elven Armor. There's also the part of the Twilight Sepulcher dungeon where you have to maneuver through an area illuminated only be several braziers without actually getting too close to them, as they will burn you to death if you do.
The Dwemer used a lot of shiny gold-like metal and glowing jewels in their technology, armour, weaponry, and architecture. They were also total psychopaths. Abusive Precursors 101.
In God of War 3, among the gods who oppose Kratos there is Helios, the god of the sun, and Hermes, who has his hair made of light. and Zeus who is a Grandpa God with a light glow One could argue that they were corrupted by the evils of Pandora's Box, but the only god who seems to have been significantly affected was Zeus, so it may just be that they are that way.
Some of the lesser foes, like the desert sirens, Perseus and undead sentries also use light attacks, throwing golden light at Kratos.
The little angelic boy named Emilio Michaelov in Psychic Force. At the first glance, he's a timid boy who just had tremendous power of light, but good hearted. Then he gets brainwashed and then turns into an Ax-Crazy psycho working for the bad guys. His good self still struggle to prevail over his evil self, but ultimately fails.
Orochi from The King of Fighters 97 who is a white pants wearing white haired Bishōnen who can call lightning from the sky and blasts his opponents with light as one of his super moves.
Golden Sun: Dark Dawn uses this trope for the Apollo Sanctum, which is bathed in light so intense it will kill your party without somebody wearing the correct equipment to provide protection. The light around the Apollo Lens is so fierce that even the Umbra Gear cannot protect the person who has to fire it. Manlytearsensue.
In Guild Wars: Prophecies, the White Mantle (dressed, appropriately, in swishy white and gold getups) initially seem like great guys. They welcome a band of refugees from a formerly-enemy country, give them a nice patch of land, spend lots of time fighting the undead menace that has recently risen, recognize (and promote) talent, even among foreigners, and search the peasantry for those with magical talents so that those peasants can be educated and their talents developed. Turns out, though, that all those talented peasants are being sacrificed to golden, floating, not-really-gods, the undead were attracted by an artifact the White Mantle shouldn't have been messing with in the first place, and other Evil Things were afoot, ultimately caused by the dark god Abaddon, who has been trying to break his prison and destroy the world since the other five gods caged him up about a thousand years ago. Their counterparts the Shining Blade, with an equally bright name but more practical clothing, are pretty straightforward, though.
The fourth generation Pokémon games give us Cyrus, a villain named after the sun (at least in most translations), who is a Knight Templar type. Depending on the version you play, he's either a straight-up Omnicidal Maniac or a good bit more sympathetic (but still evil). However, the PC's, Lucas and Dawn, also have names with light themes, so they largely avert the trope.
Team Plasma is rather strongly based on Christianity, with their Templar-like uniforms, talk about "saving" Pokémon, and use of the Chi Rho, an ancient symbol used to represent Jesus, as a symbol. They're also a deranged hypocritical terrorist cult being manipulated by a fraudulent leader in his attempt to gain power.
The Khalai Protoss of Starcraft certainly qualify. In contrast to the more kind, individualistic Dark Templar, the light-aligned Khalai/High Templar are blind, arrogant religious zealots. The Khalai are also the war-mongers among the Protoss, in contrast to the peaceful Dark Templars. During the course of the series so far, the Khalai Protoss have declared war on the Dark Templar three times, while the Dark Templar have yet to declare war on the Khalai, just wanting to be left alone.
The Khalai Protoss *do* get better though, most likely because nearly all of the Judicators and Conclave leaders were killed during the Zerg invasion of Aiur. Aldaris was the last of the "old order", and he gets killed by Kerrigan after starting another war among the Protoss. All of the Lawful Stupid fundamentalists were killed off, and only the ones more willing to change their ways and work with the Dark Templar survived.
Magical Starsign assigns a starsign to everyone, including antagonists. Most of the Space Police is of Light. And a sizeable chunk of them cooperates with the pirate otters.
The guardian faction from Rift. They're the chosen of the world's gods, live well and faithfully, yet they're genocidally zealotic towards anything that shows a sign of heresy. They're also very, very quick to lose their minds; for example, in the Defiant version of the Bad Future instance "Fall of Lantern Hook", where the world is being assaulted by Maelforge, they completely lose it and start throwing everyone, innocent, guilty, believer and heretic alike into the fires.
In Runescape, CommanderZilyana is one of the bosses in God Wars Dungeon and her master, Saradomin, in spite of being the god of Order and Wisdom, is a ruthless tyrant who can be very cruel to those who offend his sense of pride.
The final Bowser level of Super Mario Galaxy actually takes place in orbit around a giant hollow Sun Bowser created and is fought inside of.
There is also an evil Angry Sun enemy introduced in the second world of Super Mario Bros. 3 which will begin to spin around and attack and chase the player. It can be killed by hitting it with a shell. It returned to harass players in the Mario Kart series.
In Terraria, you have the hallow biome, which is a polar opposite to The Corruption, with multicolored trees and a permanent rainbow, but infects other biomes exactly the same way, and its inhabitants (which include pixies and unicorns) are just as nasty as their corrupt counterparts.
Tenchu 2 had the Burning Dawn ninjas who want to leave their life of darkness behind and embrace the light. Special mention goes to the psychopath Suzaku. He is the Phoenix and symbolizes light, flame and rebirth. He gets reborn as Onikage
There are the templars in general - an order of religious knights in shining armor, devoted to their duty of protecting the people from supernatural menace...unfortunately, this involves locking up many innocent people who have been born with magical potential. While some templars are decent, others are viciously abusive of their charges (beating, raping, or effectively lobotomizing them), and the order ends up locking most mages in solitary confinement, forbidding any contact with their friends and families, sending death squads to kill people suspected of aiding runaway mages, and attempting to kill every mage in the city at the end.
In particular, there's Knight-Commander Meredith, the faction's leader and the game's Final Boss, who is driven mad by an Artifact of Doom; her shiny armor, regal bearing, and pretty pale-blonde hair accentuate this trope.
And, on the other hand, there's Anders: an altruistic, idealistic healer mage (handsome and blond too) who lives in the city's worst slum healing refugees for free and sheltering runaway mages, constantly risking his life for his patients and charges, the cause of mage freedom, and his friend and/or lover Hawke...who is gradually being corrupted from within by an otherworldly spirit twisted by his own anger at templars and the world's injustice, and who ends up blowing up a church with innocent clergy inside in order to start the Mage-Templar War.
Mass Effect 3's Cerberus troops wear all white. They're also human-centric terrorists.
In Asura's Wrath most of the Shinkoku forces (Plus the commanders) utilize Gold and White Are Divine in their colorations, and most attacks are light based. Deus wears all white and wields lightning for his attacks. Charavartin is this even more so, by proxy of being God and the Creator and uses light as his main attacks. His Creator form invokes this and Dark Is Evil with a pure white skin color yet a black and white aura in his attacks.
In Duel Savior Destiny, everyone important is training to become the Messiah, but it turns out that the Messiah has two candidates and that if the 'bad' one wins they might destroy everything or turn the world into a land for monsters. But it actually goes beyond that: The Messiah itself is a position that dooms the world. Also, God Is Evil.
There are hints of this in the backstory of the Disciples series. The Highfather, head honcho god that the bright and shiny Empire worships, was a Jerkass who blamed the Satan expy Bethrezen for the flaws in creation that Bethrezen merely pointed out and imprisoned him in Hell. Reaches new heights in the third game, since the big reveal is that the angel Inoel sent from the heavens is the herald of the end of the world. The Highfather wants to destroy the world, believing it to be a hopeless mess, and the Final Boss is the archangel who was sent to do it. Bethrezen and his followers are actually trying to prevent this.
Mori Motonari of Sengoku Basara refers to himself as "The Child of the Sun". He's also an empathy deficient psycho, who see's everyone, even his own men, as nothing but expendable pawns to further his own ambitions.
Monster Girl Quest: Ilias pretty much embodies this trope. She (blonde haired, blue eyed, white and gold clothes, a halo, three sets of wings), the angels, and the humans embody the light as the first monster lord and monsters embody the dark. Ilias despises monsters and only wishes to keep a controlled population enslaved to keep the world in balance, and decides to wipe out humans (whom she created) as punishment for those who don't blindly follow her tenants.
Dungeon Crawl is a really good example. Holy beings such as angels are just as bloodthirsty as demons. Even if you're not actually evil they'll still attack you on sight with intent to kill and, given how powerful they tend to be, they'll probably succeed at that goal. You can't sneak past them either, thanks to their glowing halo which will illuminate you and make you easy to spot. And if you do manage to kill one of them your reward is a blast of holy fire courtesy of their god, The Shining One. That's right. You get smote with holy fire... for defending yourself.
The only characters safe from attacks by angels, daevas, and other holy monsters are followers of the three good gods, and even then it only works if your piety is high enough and the being in question isn't having a bad day. What's more, even on the off chance an angel does decide you deserve to live they'll still only become neutral, not friendly, meaning they'll still attack you if you're in their way.
Papa Blanc from de Blob 2. He poses as a benevolent religious leader decked out in white, as are his subordinates. He also uses remote-controlled drones that emit a gentle light that temporarily hypnotizes those who stare at it.
Papa Blanc is really Comrade Black, who plots to take over the colorful planet of Raydia through any means possible. His ultimate weapon is a giant version of the small drones mentioned above, the Hypno Ray, which combines the colors siphoned from the planet below. This combined color energy takes the form of a brilliant beam white light when shot back down to the planet. Using this weapon, Comrade Black can hypnotize the entire planet in a matter of about 45 minutes.
In the Shadow Hearts series, the lead protagonist is often a Dark innate character, who naturally takes more damage from holy spells. Nicolai Conrad, a priest from the Vatican who uses holy magic, is The Dragon and, of all the characters in the game, successfully deals with Yuri via the Holy Mistletoe.
In Dota 2, the Radiant team is mostly filled with virtuous heroes who fight for good. Exceptions include:
Centaur Warrunner (A Blood Knight who loves to kill, and fights to prove that he is the most dangerous warrior ever)
Anti-Mage (Who seeks to eliminate every magic user on the planet, whether they are good or evil)
Troll Warlord (A Troll taken up to eleven, to the point where even his brothers couldn't stand him)
Chen (A zealous Knight Templar who will destroy all who refuse to convert)
Ogre Magi (More Chaotic Stupid than evil, some of their equipment descriptions suggest they kill and loot random travellers)
Subverted by The Boss in Metal Gear Solid 3: Snake Eater, a defector to the Soviet Union who wears an all-white sneaking suit. However, even when she's beating the crap out of Snake in every scene she's in, the game gives her an incredibly sympathetic treatment, ending with going over her backstory and beliefs. Subverted even more when it turns out that she wasn't even a real defector, but a tragic scapegoat.
Two of the bosses in Dark Souls II have bright appearances that belie their true dark nature. Queen Nashandra initially looks like a tall beautiful woman clad in white while her real form is the stuff of nightmares. Darklurker is an angelic being who resides in the darkest depths and is as hostile as any other enemy. Ironically, one of them (likely both) is a fragment of Manus, the purest example of Dark Is Evil from the previous game.
Nagito Komaeda from Super Dangan Ronpa 2 is a total Hope Freak, presenting himself as selfless All-Loving Hero and also carrying the title of Super High School Level Good Luck, the same title as the main character from the previous game, with eventual aspirations to become Super High School Level Hope as he did. He's also one of the most Ax-Crazy characters in the series, quickly turning into a total Wild Card, whether he's trying to commit the first murder to kickstart the game, purposefully withholding information, jumping from supporting the main characters to supporting one of the killers and back again, and eventually even threatening to blow up the entire island while still ranting about hope.