Bleach: The Arrancar Arc's climax is the Deicide mini-arc, focusing on Aizen's obsession with reaching and surpassing the realm of divinity. However, his target (the Spirit King) is officially regarded as a king by most characters. The arc ends with Aizen's defeat and the death of Gin, who used his own God-Killing Spear to try and slay Aizen. Like the Spirit King, Aizen is not a god; he simply reached a power level too great for most characters to comprehend.
In Princess Mononoke, Lady Eboshi kills the forest spirit, which is a sort of Physical God. The results, however, aren't quite what she intended.
An extremely difficult proposition in Saint Seiya, as the gods (with the exception of Eris in the first OVA) are really powerful, but possible with the right means. The real problem is getting them to STAY dead: Poseidon apparently died millennia before the series, but still managed to operate as a spirit and by Grand Theft Me.
A variation occurs in Code Geass. Emperor Charles and his brother, V.V., having lost their parents to the machinations of their Deadly Decadent Court, promised each other as children that if there was a god that made people fight and scheme against each other for power, they would kill him. By the time they are older and in a position to put their plan into action, their understanding of the situation has sufficiently evolved that they're no longer trying to kill the "god" they have discovered, but they are planning to use it to enact an Assimilation Plot where all human consciousness, past and present, will unite so the fighting will stop and the dead will return.
New Getter Robo the final fight has the Getter team fighting four beings who describe themselves as gods and accomplish feats no less then bringing themselves back from death come to destroy the Getter Robo before it evolves into the terrifying Getter Emperor.
This can happen in Death Note when a Shinigami kills someone with their notebooks to selflessly save another person's life. This happens to Gelus and Rem when they save Misa's life.
It happens in Preacher. The Saint of Killers REALLY lived up to his name.
In Thorgal, Ogotai gets shot in the back with his own plasma gun. He wasn't a real god, just a dangerously delusional and terribly powerful alien psychic, but from the characters' power level, he certainly counts. And he did have a Mayincatec civilization doing mass human sacrifices for him.
Dungeon Keeper Ami is leaning towards this. Ami has discussed some plans (some even viable, apparently) for killing Metallia. It appears she may have to resort to this sooner, however, as both Crowned Death and Azzaratha, the Mighty Tyrant, are baying for her blood due to her many offenses against them and her general attitude to being a keeper in general.
The Unraveler of Mysteries has moved in opposition to her at least once, but it seems that she is less inclined to seek vengeance against Ami, and intends to study or recruit her instead.
Star Trek V has earned the Fan Nick NameStar Trek: Shoot God in the Face since its climax involves going to the heart of the galaxy and meeting an omnipotent, godlike being in need of a starship, and then shooting it in the face.
In the 2010 remake of Clash of the Titans, various rulers are trying to do this to the Olympians by destroying their temples and denying them worship. While it does weaken them, the gods are still powerful enough to inflict misery on the commonfolk, whose suffering their arrogant rulers ignore. It also doesn't do anything to weaken Hades, since he draws power from their fear of death.
The climax of Dogma involves the protagonist finding and killing Godnote God has currently taken human form, and the body is in a coma on life support, so incapacitated from doing anything, in order to allow Her to return to Heaven and appear at the place She needs to be to stop the villain from destroying the universe.
From The Belgariad Belgarion of Riva has "Godslayer" as one of his official titles, and it isn't honorary.
Also by Eddings, Sparhawk killed a god at the end of both The Elenium and The Tamuli. The gods were even aware this was a danger because Sparhawk was born Immune to Fate.
In Everworld gods can't be killed by mortal means, but they can be killed by other gods or godly weapons. Or modern weapons from our world. There's also the Eldritch Abomination Ka Anor, an alien god who eats other gods and is basically trying to genocide the whole holy race.
Immortal gods and Fae are a pain to kill. Even chopping off their head or grinding them into nothing won't keep them dead forever. Only two conditions are known where gods can surely be killed. First, when a plane of existence is created to permit it. Second on Halloween until the first birdsong is heard the next morning.
In the novel Cold Days, Harry is given an assignment to kill an Immortal, namely Maeve, the Winter Lady. He is less than pleased with this daunting task. But Murphy is the one who ends up killing Maeve. And before that, Maeve kills Lily, the Summer Lady, with a bullet to her head. According to Bob, even THIS does not technically stick. Maeve may be dead, but this just means someone ELSE becomes the Winter Lady, and is eventually becomes, if not Maeve, something very close.
Worf claims that Klingons have no gods, because they killed them centuries ago. Apparently they were "more trouble than they were worth." We later learn that this was actually a joke. The gods were really all killed almost immediately after the first two Klingons were created; this partnership is the core of the Klingon ideal of marriage.
In the TOS episode, "Who Mourns for Adonais", an alien claiming to be the Greek god Apollo captures the Enterprise. They destroy the source of his powers and he "spreads himself upon the winds" to join his fellow gods that had passed on.
In Stargate SG-1, a device is created that is capable of killing ascendedbeings. In the Ori galaxy, the Ori themselves are ascended beings who have convinced their followers that they are gods. The device is sent through a stargate to the Ori galaxy, where it goes off, destroying all of the Ori. It is SG-1's impressive tally of dead Goa'uld that starts enslaved humans and Jaffa thinking that maybe the Goa'uld aren't truly gods after all.
In "Pyramids of Mars" the 4th Doctor kills Sutekh the Destroyer, last of the Godlike Osirians who inspired the Egyptian Gods.
The 7th Doctor could be quite good at this. "The Greatest Show in the Galaxy" has him defeat the Gods of Ragnarok. In the Death Comes to Time, generally thought of as non-canon, he kills the rogue Time Lord General Tannis and seemingly dies in the process (here the Time Lords all have Reality Warper capabilities and are referred to as Gods of the Fourth).
"Bad Wolf/Parting of the Ways" has Rose do this to the God Emperor of the Daleks.
Balder is killed by an arrow (or spear) through the heart shot by Hodr, but he was set up by Loki. He knew Balder's only weakness: mistletoe. In Gesta Danorum's version, Baldr dies via a sword called mistletoe.
At Ragnarok, Odin, Thor, Loki, Heimdall, Frey, and most of the Aesir bite it at the hands of giants, trolls, Fenrir, Jormungandr, and Surtr.
In Odinani religion, every god except for the Superior one who is the origin of all things, only exists to serve a specific purpose. One that purpose has been fulfilled they die. In this case "killing" them would be a good thing, as it means you are becoming more self sufficient.
According to The Bible, the Pharisees, the Jews, and Pontius Pilate all committed this when they crucified Jesus Christ in 33 A.D.. From the same source, this act was subverted three days after its commission.
In Japanese Mythology, the goddess Izanami was killed by giving birth to a god of fire. Her husband, Izanagi, killed the child Kagutsuchi out of grief. After her death, Izanami fell into the underworld and became a zombie goddess. The Kojiki also has cases where mythical Japanese emperors fought and killed the 'gods of the earth', probably allusion to the pacification of rival tribes. However, the emperors themselves were descended from Amaterasu, the Sun Goddess of the Heaven, so these are probably cases of takes one to kill one.
In Greek Mythology, the Ophiotaurus was said to grant the power to defeat the gods to anyone who burned its entrails. The Titans managed to kill it but Zeus sent an eagle to snatch its entrails before they could be burned.
Exalted is full of exaggeration, and this trope is no exception. You can trivially kill the vast majority of gods right out of chargen. And not only you can kill typical day-to-day house-spirit gods, you can also kill the Incarnae, who are the big bosses of the gods. And ultimately you can kill the Primordials, who are thegods of the gods. In fact, that last one was the very reason why the Exalted were created.
Under the rules (Deities and Demigods Cyclopedia) it was possible to kill deities, which led to bizarre results. One example was a letter to Dragon magazine in which a PC killed the Norse Mythology god Thor by pushing him off the top of a wall and getting Thor's magical hammer Mjolnir as booty.
Module Q1 Queen of the Demonweb Pits. A high level PC group could kill Lolth, the Demon Queen of Spiders, who was a lesser deity under the rules. If they did so her spider ship would cease to exist, but they would be saved and returned to the Prime Material Plane by their deities.
Legends and Lore supplement. Deities could only be killed by a more powerful deity or any deity using an artifact. Mortals could never kill a deity. Deities sometimes created avatars (lesser versions of themselves) to act on the Prime Material Plane. Avatars could be destroyed by mortals.
In the Planescape setting, the Lady of Pain slew Aoskar, Greater God of Portals. She then killed everyone who worshipped him, razed his temple and destroyed all written lore about him and mazed anyone who thereafter joined his faith, leaving only one priest alive (perhaps as a reminder). The priest? Was one of her own servants who turned from her to worship Aoskar, which is what kicked off her deicidal fit. She bars all gods from Sigil now, though Aoskar was really the only exception in the past anyway.
Killing gods were a fairly trivial task (although it's rarely easy) in 3.5e. 4E has a few deities statted up (Bahamut, Tiamat, Torog, Lolth at least), and usually require you meet some special condition to permanently beat them down (either affecting them in some way that violates their portfolio, using something against their iconic material, or getting a bunch of Primordials/Demon Lords and having them gang up on them).
In Magic: The Gathering, It is possible to deal with the indestructable gods of Theros by exiling them in one way or another.
In a more flavorful example, Deicide is a card in Journey into Nyx that exiles an enchantment, where if you choose to exile an opponent's god, all other copies of that god in your opponent's hand, deck, and graveyard also get exiled.
Storywise, this is exactly what Elspeth does to the recently ascended Xenagos.
In Warhammer 40,000, when Slaanesh was born, he made straight for the Eldar pantheon and easily slaughtered all of them save for three. Isha, the goddess of healing, was saved by Nurgle (although given he's a Chaos god of disease who is physically repulsive in the worst possible way, madly in love with her and shows his affection by infecting her with disease, her current situation is arguably worse than death), Cegorachgot away, and Khaine tried to fight him, got his ass kicked and literally shattered into pieces, and now survives as a fragment in the heart of every one of the Eldar's craftworlds. Just a quick aside on the Isha/Nurgle thing. Yes, Nurgle does the whole 'infection' thing with Isha...but Isha in return does the whole 'curing' thing (which Nurgle does allow, of sorts).
It's actually possible to do this in Call of Cthulhu, but it's very difficult to do so. One method involves summoning the God without his consent, which pisses it off but temporarily weakens it enough to be killed by extreme means. Case in point: Old Man Henderson summoning Hastur (which was possible because Henderson was his greatest enemy at the time) and then detonating "enough explosives wired to make Michael Bay blush".
This is the purpose of the strategy games Dominions, currently in its third incarnation. You control a nation with a lesser physical god, be it a Titan, a Vampire Queen, or a Stone Monolith, as a playable unit. The goal is to eliminate all other gods and enforce monotheism, your theism. However, killing the physical form of the god is not permanent, belief will bring them back. Instead, the only way to truly kill a god is to get rid of its followers.
In Morrowind, you can kill up to three Gods, with two being required to finish the story. They are Vivec, Almalexia in Tribunal (necessary to finish Tribunal's story), and Dagoth Ur (necessary to finish the main game's story).
Killing Mehrunes Dagon in Oblivion is supposed to be impossible (he's got something like 10,000 HP and can stomp you to death without half-trying), but can be done if you A) abuse the Alchemy and Enchant skills to make a Game Breaking enchanted weapon, or B) get lucky with Wabbajack.
Shin Megami Tensei III: Nocturne has the protagonist defeat Kagutsuchi, a mere avatar of YHVH. However, by completing the secret True Demon ending, he ultimately becomes the general of a demonic army aiming to take down YHVH once and for all.
Somewhat subverted in the Digital Devil Saga series where god is the final boss and he is actively destroying the world yet the characters don't intend to kill him. They just want to ask him nicely to leave the world alone.
The Persona series continues this trend, with the main characters fighting Nyarlathotep, Nyx, and Izanami. Of course, it takes two whole games to banish Nyarlathotep (and he seems to be back as of Persona 4 Arena), you don't kill Nyx so much as seal her away, and Izanami seems rather pleased to have been defeated.
The Xeno meta-series games usually have this as a plot staple:
Xenogears's plot comes down to this, with the main party facing off against the Physical God that created "humanity" from the genetic material of actual humans millenia ago.
The Xenosaga trilogy has a different twist on this with "God" actually being a benign, vaguely supportive force while the villain is a Physical God who's taken his self-imposed role as caretaker of the universe a step too far and has begun doing more harm than good.
Xenoblade eventually leads to this, with the final showdown being against the god of Bionis and perpetual creator and destroyer of the world, Zanza. After beating him, however, the end-game cutscene reveals that he used to be a mortal human working in a research facility in orbit around Earth, meant to attempt creating a universe - set in our world sometime in the future. When he initiated the creation, the existing universe was destroyed, and he ended up being a god in the new one.
Fire Emblem: Radiant Dawn ends with Ike striking down the goddess Ashera, who petrified every living thing in the world except for those strong enough to endure it (aka, Ike and Micaiah's armies, among a very few others). However, she is not gone for good, and it's revealed postgame (if you partook in a pretty lengthy and obscure sidequest) that she returns several millenia after the game's end, merged back into her original form as Ashunera.
Also, in Fire Emblem Awakening one of the options in the Grand Finale is to do this to Evil God Grima. The other is just to seal it away, which will last for a thousand years. The catch, however? The Player Character is said God... sorta, as s/he is Grima's perfect vessel and, in killing Grima, s/he is erased from existence. Though s/he comes back later, now fully free of Grima and as a normal person.
One ending in Yggdra Union has the eponymous character head to heaven to do just that.
Sacrifice sees the five gods of the world dropping like flies as the story goes on: Eldred kills at least two in every campaign, and Marduk inevitably kills the rest. It's explained to you that the gods you killed may return with a new name later as long as there are people to believe in the forces they represent, but the process takes centuries at best.
Asura's Wrath has this as well. The Seven Deities started out as MagitekCyborg members of a race known as "Demigods" — a Human Subspecies that is descended from humans who underwent Bio-Augmentation to manipulate Mantra, an ambient Power Source for the setting's Functional Magic, Ki Attacks, and Magitek — who decided to elevate themselves to full-on godhood by assassinating the emperor and pinning the murder on Asura, then kidnapping his daughter because of her unique ability at controlling Mantra. Asura is betrayed, his wife is murdered, and he is killed. He comes back, and he is pissed.Elevated to really ridiculous levels with Asura killing Chakravartin, a being that's not only the source of Mantra, and the embodiment of the Wheel of life and Samsara, but also is stated to have been the creator of the universe itself
Final Fantasy Dissidia involves the heroes and villains of Final Fantasy 1-12 on teams for Chaos, God of Disorder and Cosmos, Goddess of Harmony. So that's a team of wannabe gods, under another god, versus a goddess and her team of non-gods who had already killed them. Although, picking a single's battle with the all-powerful God of Chaos who easily kills off his oppositeoffers some entertaining exchanges.
Chaos: Do not atone. JUST PERISH!
Record of Agarest War 2 has Weiss, the first generation protagonist who kills a god and now must pay the price. Although he didn't get to actually kill Chaos because the real Weiss has been Dead All Along.
The Sinistrals in the Lufia series claim to be gods, and they've got the power to back up that claim. They're also embodiments of evil, so the plot of the games usually revolves around finding the Dual Blade, a sword which can kill gods, and then kicking the Sinistrals' asses with it.
In Dungeon Crawl, Gods Need Prayer Badly. Gods without intelligent followers will fade away. This makes it possible to kill Jiyva, the god of slime, by killing Royal Jelly, the only slime intelligent enough to worship. The other gods have enough followers to not be susceptible to this.
In Dark Souls, you end up killing all of the deities save for the Furtive Pygmy mentioned in the opening cutscene. Granted, most of them are in pretty bad shape by the time you actually meet them. A few of the other bosses are minor gods as well, but they can be killed like any other enemy in the game. It helps that you're toting a chunk of the Dark Soul around, being a descendant of the Pygmy.
Neverwinter Nights 2: Mask of the Betrayergives you the opportunity to finish off Myrkul with the Spirit-Eater curse. This is also Death by Irony. Depending on the ending you get, you can become an unholy abomination of soul eating wrath. A large number of gods attempt to take you down as an affront to all existence but it's heavily implied that you consume so many, that they just decide to leave you alone.
Attempted twice in Bob and George with the Author, who is essentially the God of the comic's universe. At the end of the first game storyline Dr Wily captures and seemingly kills the Author, erasing the comic from existence. It was quickly established the Author was only injured and recovered (at the time this was done because the Mega Man strips were meant to be filler and the Author did intend to stop them, but then wound up going back to them and they became the main story). In the final storyline, Bob attempts the same plan but takes it Up to Eleven by arranging for the Author to get killed in three time periods, ensuring his destruction. When George points out that Wily already tried killing the Author and failed, the Shadowy Author reminds him that since it's already known the comic is coming to an end there's no guarantee Bob's plan will fail this time (it does, but the point is still valid).
In Penny Arcade Tycho recommends killing the gods of Gabe's ludicrously powerful Dungeons & Dragons group in an attempt to find something to frighten them. Unfortunately...
Gabe:They killed their gods.
Tycho: Why would they do that?
Gabe: To ingest their godseeds.
A major plot point in Digger, though it doesn't come up until late into the comic's run. Interestingly, it's actually a Mercy Kill; the god in question is not the Big Bad, but its victim and host.
Sluggy Freelance: The talking sword Chaz can kill just about anything when powered by innocent blood. It claims it could easily kill the Demon King, a God of Evil. We don't get to see this happen, but less direct contact with Chaz does scar the Demon King.
Imperial Agent: The charges against you include three counts of attempted deicide...
Callahan: One of those succeeded.
Imperial Agent: We don't have a law that covers successful deicide.
Perhaps the ultimate example would be The Salvation War series. The first story has humanity go to war with Hell and win so hard that it is later referred to as the Curbstomp War. Then we kill Satan with cruise missiles. The next story, we go to war with Heaven. The only reason that we don't personally kill God there... well... someone beat us to it.
From Atop the Fourth Wall, Linkara is against the entity which is Missingno, whom is described as an elder God. Linkara acknowledges that conventional combat does not work and only by using a Hannibal Lecture is he able to defeat the entity.
In some Transformers continuties, planet Cybertron is either destroyed or rendered uninhabitable because of a war between the Autobots and Decepticons. Keep in mind that Cybertron is actually their god Primus in disguise...