Asura's Wrath has The Golden Spider/Chakravartin. The omnipotent ruler of Gaea, he is the one responsible for the Gohma being unleashed upon Gaea and many other worlds, and makes everyone in these worlds suffer just to find his next heir. He thinks this is saintly of him, but Asura calls him out on this while punching him in the face repeatedly. The Seven Deities are a less powerful example of this. Of them, only Yasha, Deus and Augus are not outright sadistic, violent, arrogant beings who look down upon mortals and use them as they see fit, and Augus only because he cares not for domination but simply a good fight. Even Yasha and Deus was willing to be Necessarily Evil.
Bastion: The gods idols only make the game harder, in fact, there is a song called "The Pantheon (Ain't Gonna Catch You)" telling how the different gods will kick you in the floor.
Bayonetta has Jubileus, the Goddess who controls the realm of Paradiso and its Angels, and who drives the plot of the first game in that she is the story's Greater-Scope Villain, with the Big Bad's goal being to recover the two reality-shaping "Eyes of the World" to awaken her with the power to destroy and recreate the mortal world in her own image as a "perfect world". The second game makes her worse, by revealing that what she was doing was a power-grab; there are at least three Creator-Gods in the Bayonetta universe, one each for Paradiso, Inferno and Earth. Jubileus was hoping to steal the power of Aesir, the Creator-God of Earth, and use that to destroy every world that isn't Paradiso before recreating them as part of Paradiso, making her the only Creator-God to still exist.
There are hints that the voice ordering Isaac's mother to abuse him is actually Satan in disguise, furthering the subversion.
Blasphemous has the Grievous Miracle, a fickle phenomenon affecting the miserable land of Cvstodia. It specializes in granting its followers' wishes... which in Cvstodia's Martyrdom Culture, often comes through the creation of Body Horror monstrosities referencing the means through which its faithful wish to be punished for no real purpose other than making them suffer. The High Wills, creators of the Miracle, made it explicitly for their own benefit, shaping Cvstodia's culture along with the Miracle to provide them with a perpetual-motion machine of prayer and pain, and the horrible fates they visited upon Laudes, who loved their prophet more than they, and the Fourth Brother, who discovered the whole charade, show that they don't practice what they preach.
Doom Eternal: The Codex speaks of The Father, who is responsible for the creation of all life, including the Dark Lord, Davoth, who he banished to Hell and not killed out of sheer compassion for his creations. The Ancient Gods - Part Two reveals that the being known as the Father was actually a usurper. Davoth is the real Father, who was betrayed by the Maykrs, his own creations, after they had discovered the secret to immortality and sealed him and his first world Jekkad away out of fear that he would eventually end all life — and Davoth's fury would transform his people into the demons and his world into Hell. He seeks to destroy the Maykrs and creation entire as revenge for this betrayal, and was instrumental in the creation of the Doom Slayer himself. Though Word of God implies Davoth may also just be lying about all this.
Dragalia Lost: Xenos is a bit of a deconstruction. When he initially created the world with the help of Bahamut, he was optimistic about what humanity would be able to accomplish. These hopes would quickly be dashed, since humanity would continue to wage war on each other, end up wiping themselves out due to their stupidity, and repeatedly attack Xenos, hoping to seek his power. He wiped them out and gave them another chance time and time again, but every single time, they would end up making the exact same mistakes. Eventually, he came to the conclusion that humanity was completely a lost cause, and that the only way that they would ever prosper is if their free will was taken away from them. That is why Xenos wants to create a world where nobody gets to decide what their future is going to be like, and all of their choices are made for them, regardless of their opinions.
In Dragon Age: Origins, Archdemons that lead Darkspawn hordes are Old Gods of the Tevinter corrupted by the Blight. The Maker is kind of an asshole of a god, instead of just killing the Tevinter mages that attempted to breach the Golden City, he cursed them to spread devastation in their wake and sent them to destroy the mortal world.
The Legacy DLC for Dragon Age II reveals that according to the Darkspawn Emissary Corypheus, who was once a Tevinter magister, the Golden City was already the Black City when he and his fellow magisters entered it... implying that it corrupted them rather than the other way around. Which, if the Golden City/Black City is the home of the Maker, likely implies that the Maker is evil too. Considering what a Crapsack World Thedas is, that makes a disturbing amount of sense...
In Dragon Quest VII, when you resurrect God, he immediately begins an evil tyrannical regime that confuses and subjugates the newly reunited world. However, this turns into a subversion as "God" is actually the thought-to-be-defeated Demon Lord in disguise. You eventually do fight God, but it's as a superboss outside of anything resembling the plot.
In Dragon Quest IX, it turns out The Almighty is kind of a royal prick who tried to destroy humanity just 'cuz. He's also been dead for a while, and it's implied that the grotto Optional Bosses you fight are fragments of his soul. Thankfully his daughter's pretty cool.
In Duel Savior Destiny God set up a system where the forces of Ruin would invade every thousand years and require the rise of the Messiah to stop them without any regard to the massive potential casualties. It's actually worse than this: If anything, God is directly responsible for the forces of Ruin, though he doesn't lead them. He is, in fact, trying to destroy the universe and remake it to something he can understand better. He's done it hundreds of times before.
In the backstory of Dwarf Fortress (insofar as a fantasy world simulator can have a backstory), the supreme deity, Armok, God of Blood, loves conflict and creates worlds in order that conflict may occur. As the world approaches stability, Armok destroys and recreates the world anew. In a meta sense, Armok is the player, who is likely to generate a new world when their current one becomes peaceful (and therefore boring).
The regular gods in the game are no better, cursing mortals with vampirism and therianthropy, bestowing slabs containing the secret of animating the dead, and raising demons from the underworld, all in the name of creating further conflict.
The Elder Scrolls series has several types of deity, which play with this trope in different ways:
Lorkhan, the creator deity who tricked/convinced some of his fellow et'Ada ("original spirits") to create Mundus, the mortal plane, is viewed as a malevolent entity by most of the races of Mer (Elves). They consider creation a malevolent act which robbed the pre-creation spirits of their divinity and forced them into the prison of the mortal world where they experience death and suffering. (The races of Men, on the other hand, generally see Lorkhan as benevolent entity who freed the pre-creation spirits from a prison of unchanging stasis.)
Those et'Ada who aided Lorkhan in creating Mundus would become known as the Aedra ("Our Ancestors" in Old Aldmeris). Due to being severely weakened by the act of creation, they rarely influence mortal affairs directly. They tend to be worshiped by mortals, both Men and Mer, for their contribution as the "Divines" and are mostly believed to be benevolent. One possible exception, depending on the interpretation, is Akatosh, the draconic God of Time and Top God of the Nine Divines pantheon. According to one prominent theory, the dragons, including Alduin, are fragments of his being. Dragons are beings of destruction and domination, with Alduin having the responsibility of "eating the world" at the end of every "kalpa", or cycle of time.
The et'Ada who did not aid Lorkhan are known as the Daedra ("Not Our Ancestors"). Of them, the 17 most powerful are known as the Daedric Princes. Each has a particular sphere, which the are said to govern from their planes of Oblivion (the infinite void around Mundus) which they inhabit and rule. Though most are considered "evil," scholars are quick to point out that they are really beings Above Good and Evil who operate on their own Blue-and-Orange Morality. The "Good" ones only seem that way because what they seek to accomplish is generally beneficial or benevolent toward mortals, while the "Evil" ones are more likely to harm mortals with their actions. For instance, Mehrunes Dagon is the Daedric Prince of Destruction, but can be considered no more "evil" than a tidal wave or an earthquake.
In the main quest, Big Bad Dagoth Ur is a true Physical God, having tapped into the power of the Heart of Lorkhan. He channels his power from it, and has essentially become an Eldritch Abomination. The implication is that Dagoth Ur has discovered an unspeakably dangerous middle-ground between CHIM, Amaranth and Zero-Sum where he exists in a godlike state because of his awareness of Anu's Dream but, unlike CHIM where he exists as one with it and maintains his own individuality, Amaranth where he exits the Dream to make his own, or Zero-Sum where he simply fades into the Dream, Dagoth Ur's twisted, traumatized and broken mind is being imprinted on the Dream of Anu. Naturally, the Nerevarine must sever his (and the Tribunal's) ties to the Heart in order to stop him.
In the Tribunal expansion, the main quest ends with the Nerevarine having to kill Almalexia, one of the Tribunal gods. The loss of her divine power has driven her mad. She has already killed another Tribunal god, Sotha Sil, and wants you to die as a martyr.
In the Shivering Isles expansion for Oblivionyou find out that Jyggalag, the Daedric Prince of Order, became so powerful he threatened the other Daedric Princes, and thus was cursed with madness, transforming him into Sheogorath. You then free Jyggalag and take the mantle of Sheogorath.
The Creator in Final Fantasy IV: The After Years turns out to be an Evilutionary Biologist who doesn't give a damn about his creations beyond their role as planetary experiments. Vaguely hinted to be the same as the creator from Final Fantasy XIII, although, since he doesn't appear in person there, it isn't very clear in the latter how much was God being evil and how much was God not programming his biological crystal robots very well.
Final Fantasy X had the church of Yevon, who were blinded by lies and persecuted with a giant, indestructible Space Whale called Sin that was capable of leveling cities over the course of a thousand years. Yevon turns out to not be a benevolent god, but a deranged summoner who refused to die and used the souls of the last survivors of his civilization to summon a recreation of their city for them to live in forever - the same "dream Zanarkand" that Tidus and Jecht came from - via an Assimilation Plot. Sin was actually a hull for Yevon's spirit, programmed to demolish any civilization that became advanced enough to potentially disrupt the "dream" Zanarkand. Still, the true purpose of the church of Yevon (as founded by his daughter) was to appease him without letting him destroy the rest of the world for revenge. Suffice to say, this knowledge never made it past the church's leaders... until a certain Badass Longcoat who learned the truth refused to stay dead.
Final Fantasy XII has the Occuria, a pantheon of very powerful godlike spirits who have manipulated the development of mortal life on Ivalice for centuries in an ongoing Gambit Roulette, selecting and manipulating various humans as their champions, including the player characters. Ironically, they are opposed by one of their own, a rogue Occuria who has allied with the Evil Overlord in an attempt to break the Occuria's domination over humanity in a Gambit Roulette of their own, unfortunately causing tremendous misery and destruction in their attempts to do so.
In Final Fantasy XVI, Ultima is revealed to be the God responsible for creating humanity and giving life to Valisthea, and is also a narcissistic Hypocrite who condemns them for developing free will and repeating the mistakes that their own kind made, conveniently forgetting that they took their creations for granted and didn't bother to give them any guidance on their plans. Which was just as well, since Ultima never planned on sharing the world with humanity to begin with, and always planned to dispose of them once they'd outlived their usefulness.
God is the Big Bad in The Final Fantasy Legend, having created Ashura and his four fiends as entertainment for himself. And he's a little Amish man (at least before the battle starts). The most popular way the final confrontation goes down? The heroes murder God with a chainsaw.
Ares; not only did he trick his champion into murdering their own family, but subsequent games reveal he wanted to conquer Olympus with an Ax-Crazy champion, and abandoned his own son when he didn't live up to the standards of a war god. The other Greek gods got fed up with his constant raids on their patron cities and tasked Kratos with taking him out. Kratos also regresses into Ax-Crazy when he takes Ares' position, gleefully torturing and brutalizing his defeated enemies and innocent civilians for no reason beyond stress relief.
Zeus from God of War II is particularly paranoid and vengeful, attacking Kratos for the possibility that Kratos might kill and usurp him in the future. To be fair, though, Zeus was the same way in classic Greek myth, and Kratoswould probably do it. In III, it's revealed that Kratos corrupted Zeus when he opened Pandora's Box in the first game to defeat Ares. To be frank, the Gods did EVERYTHING necessary to deserve Kratos' wrath. They assumed his brother would destroy them, so they kidnapped him and made him Thanatos' prisoner. Ares then manipulates and fools him into killing his own family. After 10 years of service, Kratos kills Ares both for his revenge and their last mission, and they refuse to relieve him from his nightmares. He tries to commit suicide, but rather they turn him into the God of War. Then Kratos finds out about all Deimos, they have his mother cursed into a monster, forcing him to kill her, and kill his brother minutes after they made up. When Kratos snaps and goes on a conquest, Zeus responds by slaughtering his army, and the rebels trying to fight back against Kratos, in an arrogant display of power, and destroys Sparta just to rub it in. Really, they EARNED their karmic punishment! In God of War (PS4), Mimir outright states that the Greek Pantheon had it coming.
And throughout the series, the Greek pantheon is shown to have control over the world itself and its suffering, yet they obsess over torturing the weak, and bicker in their spare time. Those monsters that fight Kratos throughout the series? Those are created in the underworld from human souls to periodically terrorize the world of the living. Whenever the gods bicker, they wage horrendous wars with little care to the cannon fodder and civilians that get in the way. The gods killed all the Titans "for the sins of just one", then they locked up the souls that survived to be tortured for eternity, because they could.
The Asgardians in God of War (PS4). All of the lore that is found throughout the game revolves around Odin and/or Thor being ultra-racist, murderous jackasses. Mostly confirmed by their victims.
God of War Ragnarök cements Odin as a textbook sociopath who runs Asgard like a mega-corporation. Every sentence that comes out of his mouth is either a brazen lie or meant to mislead, he constantly abuses/manipulates his sons and generally views them like employees or tools (hence the reason they're all so screwed up), and frequently murders anyone who dares to resist his constant control, which includes multiple genocides. He enslaved the dwarves to make him personalized war weapons, and then used mortals as meatshields for psychological warfare. To 'hammer' in how truly empty he is, Odin murders Thor in a fit of rage during Ragnarok for daring to defy his father's increasingly brutish orders. And all of this somehow pales in comparison to a sick project he greenlit, where his unhinged fanatic cultists hung their own children, whose souls were then reforged into spirit animals and Odin's personal spies.
Record of Agarest War has the six Dark Gods/Goddesses, five of which are sealed within the false world of Agarest's five pillars located on each of the five continents. Mercury for Lucrellia's pillar, Mobius for Graccea's pillar, Deeth for Fendia's pillar, Nemesis for Enhambre's pillar, and Mayastia for Aegisthus's pillar. The sole exception of the six is Chaos, the highest among them, though despite his title, he is not "completely evil", since while he embodies his title, he is sealed in the Boundary Plane, a realm of existence outside of Agarest. He still can be considered "evil" for what he intends to do to roughly gouge out the "truth" of Agarest in his own image, had the Oathsworn legacy and their trusted companions not stopped him.
Shin Megami Tensei is, interestingly, a case of both this and God Is Good. YHVH is a complete and utter megalomaniac who demands full respect and worship from man, and if they don't provide such, His wrath follows quickly. In many games, the Law path that YHVH patrons results in a variant of the World of Silence, where all creation does nothing except ceaselessly chant prayers to Him for all eternity. However, later games reveal this to be a case of Not Quite the Almighty: YHVH, though very powerful, is only an avatar of the "Great Will", an even greater being that governs the laws of the universe. The Great Will is (debatably) a pretty straight case of God Is Good, even orchestrating YHVH's downfall when he goes mad with power. Atlus has claimed that they're moving away from this trope to avoid offending heavily-Christian countries now that they have a wider audience — though by "move away", they apparently mean "be a touch more subtle about it".
Shin Megami Tensei II marks YHVH's first appearance in the series* though he previously played a similar role in Megami Tensei II, and it makes sure to hit the ground running. This game provides the page quote, but that provides only a taste. YHVH's master plan is to exterminate all life on Earth, save for the scant few "true believers" he determines worthy of salvation. This includes most of the Messians, who experience an existential crisis upon learning that even their slavish devotion wasn't slavish enough. This is so monstrous that even on the Law route, you and Satan are so disgusted by YHVH's actions that you turn against him at the last minute.
This game additionally pulls a two-for-one, as there are two YHVHs in this game: one is a fake god created by the heretical beliefs of the archangels and the Messian leadership, and is as evil as you would expect their god to be. You defeat it about two-thirds of the way through the game, only for the real YHVH to appear and reveal himself to be just as evil as the fake.
In Nocturne Lucifer states that YHVH (or possibly the Great Will) is responsible for the Conception cycle that condemns worlds to an endless cycle of destruction and rebirth, with each new iteration meaning the deaths of everyone in the old world that is replaced. Furthermore, it's implied that YHVH did in fact deliver on his threat in the page quote, as Hijiri is stated to be trapped in a Fate Worse than Death that sounds very similar.
Although God Himself doesn't appear in Shin Megami Tensei: Strange Journey, those acting in His name are no better than He ever was, and the Law ending results in a World of Silence as per usual. In addition, the Demiurgesidequest makes the interesting claim that, contrary to Gnosticism, the Demiurge and God are one and the same. While it's implied the Demiurge becomes somewhat more reasonable after you defeat him and allow another piece of YHVH to merge with him, he's still more or less an Ax-CrazyKnight Templar who has you take him to Mem Aleph so he can participate in killing her in the Law Path and warns you very severely there will be consequences for not choosing his way in the other paths. He's also flat-out stated to have forgotten his love for humans and trampled the Goddess-worshipping world, meaning he's still an attention-hungry bastard.
Strange Journey Redux brings a new and characteristically evil incarnation of YHVH to the table: Shekinah, the true identity of the Three Wise Men. She seeks to create the World of Law... By replacing the old one, annihilating most humans and stripping the few remaining of their free will by forcing them to endlessly worship her, not dissimilar from the Law ending of the original game. She even manages a Kick the Dog moment in her final battle, where she forces Demeter to sacrifice herself just to give Shekinah a bit more juice, even though Shekinah promised her a place in the new world. Additionally, on the Law route Alex reveals herself to be a time traveller from the world created in the Law ending, and confirms that those who resist Zelenin's Mind Control are subjected to a genocide.
The original release of Devil Survivor implies that God is a bit less evil, given His actions on the behalf of humanity this go-round. The Updated Re-release of Devil Survivor, however, again throws doubt upon God's motivations by revealing He deliberately set up the Abel And Cain scenario in order to create the first martyr and the first murderer. He will also treat the player much more harshly if they take Naoya's route. While God is certainly understandable in His fear of the King of Bel and his desire to get rid of them, in the new 8th day His method of doing so is to threaten the people in the city into hunting you, in order to prey off of your empathy as they beg you to let them kill you so they can be spared. When that fails, he sends Metatron to flatten the city in its entirety, and when THAT fails, he's all too willing to destroy the planet altogether, Even then, this is downplayed compared to the mainline series, as he only becomes overtly evil if the player directly opposes Him. If you stick with the Law path God is happy to send assistance your way, and even if you go down a Neutral path God and His servants are mostly willing to leave you alone.
Shin Megami Tensei IV has the DLC episode "Ancient One of the Sun" which pits the protagonist against the Ancient of Days, one of God's Names. The Ancient of Days has arrived to kill off all the inhabitants of Blasted Tokyo, effectively committing genocide so that "God's Chosen" can inherit the Earth. Without the DLC episodes it is actually ambiguous about if God is evil or not, at least as far as Normal Tokyo is concerned and God's plan got derailed completely at Infernal Tokyo due to Kenji killing off the angels before God's Wrath could be unleashed.
Shin Megami Tensei IV: Apocalypse has YHVH as the Final Boss that must be beaten in both routes to stop him from oppressing humanity. God Is Evil is a firm belief among the Divine Powers, who seek to create their own universe that will be free from YHVH's machinations. Krishna explains that Both Order and Chaos are Dangerous because of YHVH intentionally setting up the universe as a stage for a faked Forever War, but points out that order and chaos by themselves are not bad things.
This is touched upon in The World Ends with You, as whether or not the Composer of The Game is simply just giving a reasonable chance to everyone for their lives again or is rather a complete Jerkass sadist who likes pitting people against each other with the risk of losing their existence. At any rate, it's a rare case where the Jesus-figure is undeniably an asshole.
Xenoblade Chronicles 1 has the Big BadZanza, the God of Bionis; a complete and utter bastard who, after destroying the entire universe, has led the world he created to an apocalypse multiple times so that his creations, which he relies on to exist, don't leave the world and expand to the stars.
The main Big Bad, Z, created a world of "Endless Now", forever stagnant and unchanging, with all of humanity eternally dying and reincarnating in two evenly matched armies that fight a Forever War for no reason. Near the end of the game, the characters ask why he made it a world of endless bloodshed and conflict, rather than, say, one where everyone is eternally happy, and he sadistically replies that he considers the bloodshed entertaining. And when it becomes clear he's losing the final battle, he decides to try to erase all existence rather than face any kind of change.
In the Future Redeemed DLC, which serves as a prequel to the main game, the main Big Bad is Alpha, who seeks to destroy the world Z created, and whom Z refers to as "my God". Making this more disturbing is that Alpha is very clearly Alvis, the Big Good of the original game, who was superior even to Zanza. It turns out that Alvis split into two beings: Alpha is himself purged of all empathy and compassion, thus why he has become evil. His cast off emotions form into an alter ego calling itself "A", who opposes Alpha and helps the heroes much like Alvis did against Zanza.
Xenosaga has a subversion. While Dimitri Yuriev believes the Dimension LordEnergy Being U-DO is evil, and it does have a tendency to cause people to go insane when it touches their minds, it isn't evil, just alien.
Mortal Kombat let's just say doesn't exactly portray its gods in the best light.
The Elder Gods certainly qualify; while hiding behind an Obstructive Code of Conduct of non-interference with their own creation, they've either downright ignored imminent threats to the Realms and breaking of sacred laws (like they did with Shao Kahn's invasion of Earth in MK 3), or manipulated proxies into doing their dirty work through elaborate Gambit Roulettes that have as much of a chance of succeeding as a snowball surviving in the burning heart of Hell, with wonderful non-rewards for doing a "good job" (have pity for Scorpion and his family and clan, or Taven and his family and friends). And when one of their own does decide to interfere, they're punished violently, regardless of whether their intent was malefic or innocent. Makes you wonder why no one's gone up there to kick their deific asses, yet...
Of particular mention when it comes to the Elder Gods is Shinnok and Cetrion, with Shinnok being one of the main villains of the franchise with tons of horrible crimes under his belt, also while Shinnok is a traitor he did still commit evil actions during his time as an Elder God. Cetrion is not much better as she betrays and kills all her fellow Elder Gods and was secretly a mole for Kronika.
Even Raiden could also qualify, depending on the game. In his Armageddon ending, he became increasingly aggressive in his protection of Earth, going as far as to destroy all other realms (both threatening and non-threatening ones) to prevent them from being a danger to Earth. And in his ending in the original game, Raiden wins the Mortal Kombat tournament, but soon becomes bored with human competition and invites other gods to participate in the tournament, which ends up destroying the planet.
The Elder Gods are motivated less by malice and more by fear of the One Being, the true supreme being whom they rebelled against and separated into the Realms. Everything they do is meant to keep the One Being from ever coming back. The One Being would qualify as an example of this trope as well, since the reason the Elder Gods rebelled against it was because it was eating them (and would likely do the same to everything else in creation if it came back).
Mortal Kombat 11 reveals that The One is NOT the only Titan. The game's main antagonist, Kronika, is the Titan of Time (and the mother of one of the Elder Gods). Her ultimate goal is to set up a Forever War that ensures neither side will ever win, and will hit the Reset Button when she doesn't get her way. Repeatedly. Scorpion's ending reveals images of other Titans who also mess around with mortals, and are the reason why his family's death is a fixed event in time.
Odin in Valkyrie Profile 2: Silmeriais ready to destroy the entire mortal world rather than face the possibility that humans will stop serving the gods unquestioningly. Lezard doesn't seem that bad all of the sudden. He is somewhat Lawful Evil in the first Valkyrie Profile, too. After all he is fine destroying the order of the mortal world by stealing its sacred treasure just to have a mighty artifact for himself and to help Lenneth to recruit more Einherjar.
Odin and the other gods are also shown to be completely apathetic towards Midgard. They sit on golden thrones in magnificent castles, while the world underneath is one of the darkest, most dismal worlds you can imagine.
Star Ocean: Till the End of Time has Our Heroes daring to enter the Time Gate into the 4th dimension, to thwart God's plans to eradicate the Milky Way and establish independence. In the climax, it turns out that the fourth dimension is full of super-advanced apathetic humans, who created our universe as a combination of reality TV and role-playing games (Earth's mythical heroes were player characters). "God" is a corporate suit who's reformatting parts of the program, seeing humanity's attempts to practice "symbology" (programming code) as some kind of bug in the system. And what truly makes this "god" evil is that when he finds out that humans have been practicing Symbology, rather than painlessly deleting them, he sends the "angelic" hordes to wipe out humanity. Maybe he thought it would boost the ratings...
In Drakengard, The World Is Always Doomed because God Is Evil. The gods that the hierarchs in the Crystal Dragon Jesus religion pray to for salvation are in fact the ones trying to destroy the world. When they show up towards the game's finale, they appear as giant, man-eating babies. Yeah. As far as who created the world, the debate is out whether the gods did or the dragons did.
Drakengard 3 sheds some light on the Cult of the Watchers and exactly what it is that they're worshiping. The goddess that the cult worships is none other than the Intoner One, with the cult being started by her Opposite-Sex Clone "brother" in order to honor her after her death. While One is a benevolent individual, as an Intoner she is destined to destroy the world unless she and her sisters are killed.
The RPG H-Game "Monster Girl 1,000" has True Goddess Eris as this, through and through as her entire plan is to remake the world by cleansing it completely of all humans and monster girl-kind. The intro and a later event specifically showcases just how disgustingly-rotten she is when she declares this to her subordinates in a meeting they attend.
Viking: Battle for Asgard: You know Freya? Yeah, she's kinda evil. The kind of evil that brings you back to life with the promise that she'll give you a chance to enter Valhalla if you kill someone for her and then realizes the benefits of having a personal assassin and promptly stabs you in the back. Skarin was not pleased and suffice it to say, it did not end well if you happened to be a God.
In the Rance universe, the creator god is a giant whale who created all of existence just to watch people fight and kill each other in wars. So Humans Are Bastards because it is Inherent in the System. And entertaining, apparently. At the end of the series, said creator decides to incarnate himself as a mortal being (as one of Rance's children, no less) just to experience things from a new perspective, and winds up learning empathy and how to care about things other than slaughter and despair. As a result, he abolishes the system of constant warfare and decides to give peace a chance instead.
It's revealed in Fire Emblem: Radiant Dawn that the setting's Top Goddess, Ashera, is a hypocriticalHolier Than ThouKnight Templar who intends to destroy humanity in order to put an end to war (while ironically allowing the real villains behind said war to live with her blessing). She does, however, have a Freudian Excuse: aghast at accidentally destroying the world with a Great Flood millennia ago, she removed all her emotions and placed them in a separate being, leaving herself impossibly cold and uncaring. The game's Distant Finale reveals that she and the being composed of her emotions (who served as the Big Good of the game) will eventually reunite into a pure good goddess.
Tales of the Abyss plays with this. From the way that all life in the world is bound by a prophecy that will eventually kill all life in the world created by the local Crystal Dragon Jesus, Lorelei, it seems that God is going to be the single most horrific tyrant imaginable. Turns out that's wrong. Lorelei didn't "create" this fate of destruction at all. He merely foresaw it and clued his follower, Yulia Jue, in on it because he believed that humans were special enough toScrew Destiny and save themselves from the destruction he had foreseen. Unfortunately, in what is almost certainly a dig at religious fundamentalists, it turns out that the order set up around Lorelei completely missed the point of what he was trying to do after Yulia's death: giving the impression for 2000 years that Lorelei wanted everyone to submit to the prophetic Score rather than overturn it.
In the Legacy of Kain games, the Elder God is in many ways the Big Bad of the series; it tells Raziel it resurrected him and that its Wheel of Fate is a force of life, but the time-travelling Raziel notices that it seems to grow as the land deteriorates, and eventually concludes that it parasitically feeds on the souls of the dead and manipulatively causes death and destruction in order to provide itself with fresh souls. However, since serious questions are raised about the full extent of its power (Raziel suspects that it might have simply been there when he recovered of his own accord and simply claimed responsibility for his survival, and it heavily relies on agents for much of its success,) it is debatable whether it can really be considered a god, especially since Kain takes the supposedly omniscient being completely by surprise and kicks its ass at the end of the series.
The Golden Sun series subverts this. Yes, the Wise One can be a very harsh taskmaster and is not against setting people trials that would shatter lesser minds. However, it has a very good reason for being something of a Knight Templar: namely the fact that it's already seen what kind of Crapsack World Alchemy can create. As such, it wants to make damn sure that it's used for good and that nobody screws the world over again with it. Now, the actual Ancients on the other hand - who possessed even greater power, given that they created the Wise One are far more morally ambiguous given that they were the ones who ruined the world in the first place. The Wise One is in fact simply a powerful golem created for the purpose of keeping Alchemy sealed. The reason it went to such lengths was because it was re-evaluating its original directives in light of new information (mainly that keeping Alchemy sealed would doom the world to a slow death anyway), but needed to make sure that people were ready for the potential problems Alchemy would bring if it was brought back.
Subverted in Knights of the Old Republic II: The Sith Lords. Kreia believes the Force to be an evil god that forces the Jedi and Sith to war with each other for eternity for its own amusement. Yet all evidence in the game and other Star Wars material pretty clearly suggests that this isn't true; even if the Force is sentient (which is debatable) than it has no influence on what mortals do with its gifts. The implication builds to be that Kreia is simply unwilling to accept her own flaws and sins, so she instead chooses to pass off the blame to some vague force in the sky. Further her stated solution to this (destroying the Force) is noted to be absolutely insane and would likely kill every living being in the galaxy since there's a trace of Force presence in all life.
An alternate interpretation of Kreia's beliefs is that the Force is not a god, but may as well be treated as one because it is composed of the connections that people constantly create between each other and the consequences that ripple throughout the cosmos. As for the evil part, the Jedi and Sith would, by natural selection, favor select courses of action that would strengthen the Force and therefore themselves, and since the most effective way to make varied peoples of isolated communities make interpersonal connections of politics and commerce, interest and fear, love and hatred, across distances measured in lightyears, is to instigate a warbetweenstars... well...
Onimusha: In this game's verse, the Creation Myth is different than the usual world. The Genma race was the one that existed since primordial chaos and then sired mankind as a Slave Race for their own, and they think it existed only as nourishment and slave for them. And their leader, Fortinbras, wants to make sure that it stays that way, when the humans started gaining free will and rebelled against it.
G.O.D.: Heed the Call to Awaken: The humans victorious against the aliens and their leader Ra Mu are faced with a being, or rather presence, calling itself God, and claiming to have been around at the beginning of the universe, when it finally reveals itself and makes its move. God itself (which is a mere conciousness) refers to the title of the game, all of you having gone through a process of 'growth or devolution'. It is the plan of such an entity, to obtain a perfectly honed body at long last, and this body will be chosen from among your party. Your party is then "offered" to be spared the destruction of the present world, and will be the only ones conferred such a privilige.
Lawful Evil in the first Valkyrie Profile, too. After all he is fine destroying the order of the mortal world by stealing its sacred treasure just to have a mighty artifact for himself and to help Lenneth to recruit more Einherjar.
