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Batwoman: Has the Religion of Crime Sect. While the regular church falls under Religion of Evil, the Sect that recurs in the series falls under this trope. The leader, Kyle Abbot broke off from the original group because a difference of ideals (that and the original group's association with Apokalips would lead to disastrous consequences for the earth). While they still worship Crime, their doctrine isn't elaborated on, and Abbot always appears as an ally to Batwoman in her ongoing, standing with her against the monsters summoned by the Big Bad and even bringing the whole sect to aid her in the final battle.
In the classic Star Trek/Babylon 5 crossover story, A Thin Veneer, the Ashen are an offshoot of the Minbari who worship the Vorlons as Gods. Their religion tells them that they are the most superior beings in the Galaxy because of this, and that they cannot be defeated thusly. They hold onto this view even as the Federation constantly curb stomps them.
The Star WarsExpanded Universe has the Yuuzhan Vong, who are in the market for a new galaxy and have just found this very nice one in which most of the inhabitants happen to depend on one of the central heresies of the Yuuzhan Vong religion—the use of non-organic technology. (They all have quite the wrong understanding of pain- pain is sacred and to be cherished, not avoided!) The solution? Mass xenocide. So it goes.
The various cults from the Cthulhu Mythos tend to fit this rather well. They're not usually evil per se, just like their gods aren't actually evil (exept for Nyarlathotep, and he's more of a dick than truly evil). According to one cultist being interrogated in Call of Cthulhu, the cultists wish for the Old Ones to return so that they can make mankind like them, unbound by law or morality, and free to dance, laugh and kill as they see fit.
Thulsa Doom's Serpent Cult from Robert E. Howard's Kull stories (as well as some adaptations of Conan, such as the movie which was originally to be about Kull anyway).
In Alan Dean Foster's The Damned Trilogy, "The Purpose" is a religion promoted by the bad guys in which all sentient life in the Galaxy comes together in cooperation by abandoning freedom and free will. And the purpose of this cooperation? To force those species who don't necessarily want to be a part of the Purpose to join up or die.
The Howlers from Animorphs may count. Their "god" really isevil, but a theme of the novels is that no sentient species can be Always Chaotic Evil, forcing him to resort to this. Essentially, the Howlers are able to slaughter every other race in the galaxy without mercy because they have the minds of children and no idea other species have any sentience of their own.
Live Action TV
In the Doctor Who episodes "Bad Wolf" and "Parting of the Ways", the Daleks seem to be worshiping the idea of their own perfection. The fact that the Daleks have a concept of blasphemy absolutely horrifies the Doctor.
The Goa'uld and their followers in Stargate SG-1 fit this trope pretty well but the Ori fit it even better, all the way down to disputes over the meaning of symbolic passages in the very King James-sounding Book of Origin. The Goa'uld aren't so much dogmatic as create dogma around themselves to control their underlings. The Ori, on the other hand...
In Star Trek: Deep Space Nine, the Jem'Hadar worship the Founders of the Dominion as gods, and see the war on the Alpha Quadrant as a holy crusade. The Founders are said to have an innate need for order and conformity, and the avowed mission of their crusade is to bring this order to the untidy quadrant-next-door.
The Minbari war against humanity was seen as a crusade to avenge their "holy leader" after his death in a botched First Contact encounter.
On a lesser scale, an alien couple murdered their child after he underwent surgery, because their faith declared that cutting into their body made him lose his soul.
The Soldiers of the One in Caprica are a monotheistic cult in a polytheistic society that believes in absolute black and white morality, and some of their branches are perfectly willing to commit suicide bombings for their beliefs, while the others quietly approve of their actions. Later the Cylons inherited the religion and used it to justify the attempted destruction of the human race in Battlestar Galactica.
In Warhammer40000, the Church of the God Emperor is the main inspiration of its many followers to go to war, and a secondary inspiration for many other factions. The Church is xenocidal and imperialist, and as happy to wipe out a wayward billion of its own people as it is to exterminate entire alien races, sometimes even for a perceived slight.
Eldar also have their own Eldar-centric religion. Eldar religion (or the surviving bits of it) has essentially two parts: one requires Eldar to survive at all costs until their new god can emerge, namely costs callously paid in billions of lives of other species, and the other part consists almost exclusively of war and murder.
The Tau are arguably a subversion, being a race of Flat Earth Atheists in a setting where literal daemons are an active force. They are regarded by the Imperium as being completely heathen, believing in no supernatural forces whatsoever. However, they are also philosophists, following strongly to a collectivist creed of striving for the Greater Good, believing that they should share this philosophy with every other sentient in the galaxy and that Utopia Justifies the Means in doing so. This tends to put them squarely into Scary Dogmatic Aliens trope, but with the twist that their dogma is secular in a setting where supernatural forces are real.
And then of course, there are the Chaos gods, who have almost as many religions as they have followers. Some believers actually believe they are doing the right thing by breaking away from the Imperial dogma, others are in it solely for the Rape, Pillage, and Burn. Even among each other they don't hold each other as being holier than others, Khorne famously does not care whether the blood of his followers or his enemies is shed in battle, and often sics his own daemons on favored followers to test them.
The Zerg from StarCraft exist for no other reason than to assimilate any species that improves their genetic stock that they encounter on their interplanetary crusade. Every sentient Zerg on the upper levels of the Hive Mind exists to participate in a religion centered around their overarching consciousness, the Overmind. The first partially free-willed consciousness that enters the Zerg Hive Mind apart from the Overmind itself (Kerrigan) eventually breaks away from the Overmind and becomes wholly and unapologetically evil while constantly lampshading the fact.
Originally, the Tal'darim protoss faction from Starcraft II were the Knight Templar flavour of this trope, in that they were territorial and aggressive and felt no remorse about killing the player's forces in missions pitched against them, but they had the legitimate grievance that the protagonists were explicitly showing up to steal their artifacts and possessions to sell for profit, and the beings they worship, the Xel'Naga, are definitely benevolent entities. They were pretty much the Lawful EvilBlack Sheep of the protoss race, who are otherwise reasonable, honourable and stand-up people. At least they were until the Heart of the Swarm expansion pack, which clarified that they worship the Token Evil Teammate of the Xel'naga pantheon - Amon, the Fallen One, which upgraded them to a Relgion Of Evil.
The Eternal Doctrine and the Path of Now and Forever from Star Control, both of which treat Ur-Quan security as paramount. The Kzer-Za's Path of Now and Forever decrees that every species is a threat to the Ur-Quan (because it might someday become too powerful if left to its own devices) and therefore must be subjugated. The Kohr-Ah Eternal Doctrine is similar, except its answer to these threats is not subjugation, it's annihilation. It's all good, though — since they believe in reincarnation, species they "cleanse" will have a chance to be reborn as Ur-Quan eventually.
Their respective philosophies are a direct result of their former slavery to the Dnyarri, who used genetic engineering to split one Ur-Quan species into two. The Kohr-Ah were soldiers, and their Eternal Doctrine reflects their simple worldview - eliminate any threat. The Kzer-Za were administrators and scientists and do not discount the benefit of having slave races and have a better understanding about controlling them. When the Kzer-Za armada surrounded the Syreen fleet (all that remained of their race) and received their surrender, they went out of their way to find them a suitable planet as the new Syreen homeworld. Also, instead of destroying all Syreen ships, they mothballed them, just in case.
The Children of Atom and the Apostles of the Holy Light from Fallout 3 are a sort of subversion: both have an unhealthy relationship with radiation, but they're a nice, good religion.
Well, the Children of the Atom are harmless. The Apostle of the Holy Light, on the other hand, had taken to handing out water imbued with lethal levels of radiation to unsuspecting travelers without their knowledge, because they believed that irradiating their bodies would save their souls.
The Covenant are out to Kill All Humans because their religious leaders have declared humans to be an affront to their gods. It is revealed in Contact Harvest that humans were the chosen inheritors of The Forerunners whom the Covenant base their faith upon. Widespread, this knowledge would have either undermined the power of the Prophets or caused societal collapse.
The Order from the Silent Hill series either falls under this trope or under Religion of Evil. Sure, their leaders Dahlia Gillespie seems to want and Claudia Wolf definitely craves a paradise for all humanity, but members like Leonard Wolf take a far more militant and unforgiving stance while even Dahlia gets at least a little giddy at the thought of a violent apocalypse. Plus it doesn't help the argument that the Order is well-intentioned that in Silent Hill 4 it's revealed that the Order runs an Orphanage of Fear that makes the Oliver Twist orphanage look like the fireworks, candy, and puppy dog store.
Supreme Commander the Aeon Illuminate who follow a religion called The Way, their main goal is to spread the way to humanity, but are willing to cleanse all non-believers.
Many Daedric cults in The Elder Scrolls series fall under this. The cults are generally reviled by the populace which worships the Aedra, likely because many of the Daedra represent rather disturbing concepts, like Destruction, Madness, and Rape.
Sins of a Solar Empire the Advent who's religion is called the Unity, which involves biological enhancements and psychic powers. Their primary goal is to exact vengeance on the TEC for banishing them thousands of years ago.
The various Abyss-worshipping cults in Fatal Frame. They don't even consider whether Abyss is good or evil, only that it hungers and must be satiated with sacrifices. It doesn't shepherd its followers to good or to evil, only that the sacrificial rituals are conducted properly. The failure to do so causes Abyss to go out of control. The main characters of this series are unfortunate strangers who are somehow qualified for sacrifices, and must fend off worshippers-turned-ghosts.