God spends most of Angel Sanctuary holed up in a tower away from the rest of the universe. Turns out to be evil, though.
Mamoru Oshii's Angel's Egg is actually about God forsaking the occupants of Noah's Ark after starting the Flood but never allowing the waters to recede.
In the shonen-ai manga Innocent Bird, God is not there, and the angels have taken over in the least likeable manner. However the devil is still evil, yet everything in between appears to have a limited choice as in - they can act how they want but their side will try to punish them.
The Transformers wind up finding their god/creator Primus midway through Transformers Cybertron after who-knows-how-long. How they missed the fact that their planet turns into a robot is also unknown.
Angel Beats! takes place in the afterlife, and there's a violent Angel wandering around, but God doesn't show himself; whether he actually exists is unclear for most of the series. It's eventually revealed that there used to be a God, but he seems to have turned into an NPC, or something. "Angel" is actually not an angel, but a regular person who has partially reprogrammed herself. The former God apparently deified himself in a similar way.
While Yashima of Kamichu! is not the God but one of an enormously large number of Shinto gods, he goes missing some time prior to the start of the series, so that Yurie has to go looking for him in the second episode.
In Bloody Cross, God has apparently disappeared or is otherwise gone and various "God candidates" are competing against each other to gather "God's inheritances", artifacts that contain some of God's power so that they can use that power to become the new God.
God has not yet bothered to show Himself in A Certain Magical Index. Given that Gabriel and the other angels have been shown to exist, it's reasonable to assume God does too. Some speculation abounds that the hero, Touma, is God's unwitting Spanner in the Works in the conflict, since Touma's power seems to be a mystery to even the most knowledgeable characters in the series, and is speculated to be of divine origin.
Kami-sama no Inai Nichiyoubi introduces us to a world which was abandoned by God fifteen years ago. Because of this, no new human beings are born and people who die don't stop living unless buried by a certain type of gravekeeper. The reason for His absence is still unknown.
Preacher. When God ends up creating something just as powerful as he is, he abandons ship, leaving Heaven to clean up the mess. When Jesse finds out about this, he decides to track down God and deliver the crunchiest of beatings.
Spawn has God disappearing for four years, and the archangels keeping it secret.
One arc of The Authority has God returning after an absence of billions of years. He's not too impressed to see his retirement home's been overrun by termites.
The Sandman: Morpheus is kept captive between the years 1916 and 1989. During that time the dream world runs wild.
An entire arc is spent resolving the fate of Hell when Lucifer quits and gives Dream guardianship of the keys to the gates. In essence, Dream chooses the next ruler of Hell. A pair of angels take over by direct command of God, and resume business as usual, except with the end goal of redemption, rather than punishment.
In Mike Carey's Lucifer series, God admitted that He had set up all of history from Creation onward as training for His hand-picked replacements - Lucifer and Michael (ironically, Michael the Good Boy proved to be a disappointment to Him). When that didn't work, God abandoned the universe, which immediately began to disintegrate from lack of Divine Will maintaining its existence. The universe was saved by Michael's daughter Elaine taking over as the new Supreme Being.
In Bone, the dragons (which are not technically Gods, but they're the series' Big Goods and are very long-lived creatures well in touch with the spiritual forces of the Bone Universe) end up going underground to sleep instead of protecting the Valley people or attempting to do anything about the Lord of the Locusts.
In one Ghost Rider story it was revealed that God's throne in Heaven is empty. Curiously, a Fear Itself tie-in reveals that Satan's throne is also empty. It is shown Lucifer is real, but Satan is more of a title no hell-lord is strong enough to claim.
Dogma puts the responsibility on the shoulders of the main characters after God seemingly vanishes from Heaven. Then again, it's not exactly as if it's her fault in this case.
Two Of A Kind begins with God coming back from one of these absences, discovering everything has gone to pot while he was gone, and deciding it's time to wipe the slate clean and start over again.
Begotten opens with the grisly scene of God Killing Himself (that's the character name according to the end credits) via disembowelment. Mother Earth emerges from his body and uses his sperm to impregnate herself, giving birth to Son Of Earth - Flesh On Bone. Mother and Son encounter faceless dwarves who first worship them and then brutally murder them. Plants sprout from their interred bodies, implying that life goes on but presumably without gods.
In Bruce Almighty God takes a couple days off, the reason? Because he was sick and tired of Bruce moaning all the time. God only left Bruce's home city, though.
It's implied that this isn't the first time that God did this, when Bruce commented on him taking a break he replied by saying "ever heard of the Dark Ages"
The resident Weird Religion Guy in Major League gets fed up asking his god for help, and prays the following before his last at bat in the big game: "I'm pissed off now, Jobu. Look, I go to you. I stick up for you. You don't help me now. I say 'Fuck you,' Jobu, I do it myself." He hit an impressive home run.
This is Sybok's motivation in Star Trek V The F Inal Frontier, and he drags the Enterprise to the center of the galaxy to find Him. He, however, is not who He seems to be, so it all ends in tears for him.
In What Dreams May Come (much of which takes place in the Afterlife), we have the following exchange:
Chris Nielsen: "Where is God in all of this?"
Albert: "Oh, He's up there. Somewhere... shouting down that He loves us. Wondering why we can't hear Him. You think?"
In The Belgariad, all the gods pick a people except Aldur (he gets a few disciples later on) because he loved the world itself too much to tie himself down. This leaves a whole bunch of people godless, and they do various stuff to fill the void. (Worshipping demons, that sort of thing) then one day one of the Godless finds out there's ANOTHER god that didn't pick a people, so he goes looking for him, and eventually embarrasses him enough so that he accepts him.
In The Malloreon, this becomes much more nuanced. The Godless actually split into several different groups: The ones mentioned above became the Ulgos (followers of UL); the ones to the south became the Dals, who explore the more esoteric magical mysteries of the world; the ones to the north became demon worshippers (and split into the more 'civilized' Karands who gave it up partially and the Morindim who still do it extensively); finally, the Melcenes to the east were actually the first of any people to form a civilization, and they remain happily godless. At the end, it turns out that there was yet another deity who hadn't arrived yet, and this time he's supposed to be everyone's God.
In Dune Messiah the Reverend Mother Gaius Hellen Mohiam asks Emperor Paul-Muad'dib Atreides if he believes in the God whose Word forms the basis of his right to rule. His answer comes out to "eh, maybe", as he (correctly) judged that they were trying to undermine his religion. Considering that the Bene Gesserit manufacture religions to suit their needs, they were being blatantly hypocritical.
So Long, and Thanks for All the Fish has Arthur and Fenchurch traveling to a far-off planet to witness God's final message to his creation: "WE APOLOGISE FOR THE INCONVENIENCE", written in giant flaming letters.
The His Dark Materials trilogy has the entity that everyone thinks is God- actually just the first angel, too old for anyone to contradict him, reduced practically to nonexistence after millennia of rule. Still, his followers fight on in his name, generally making a mess of things on Earth.
The gods of Krynn in the Dragonlance novels abandon the material plane after the knight templars start acting like they command the gods, rather than vice versa. They come back after being sought out, only to vanish again when someone steals the world from them. Naturally, that doesn't stick, either. On an interesting note, this plane is a lot more understanding to atheists than most Dungeons & Dragons settings; because really, who can blame them?
In the Incarnations of Immortality series, God is physically present, but too busy admiring Himself to pay attention to anything else. This results in the other Incarnations impeaching Him, removing Him from office, and making a rather creative choice of a new God.
One of them wins divine ascension. One earns freedom. One gets a Fate Worse Than Death. The other one just gets death.
God's Debris has this as the origin of the central philosophy: God destroyed himself in the Big Bang, and all matter, energy, and probability is God's debris.
In Alan Campbell's The Deepgate Codex series, Ayen, mother and queen of the gods, has exiled all of the other gods from Heaven, and locked its gates against both gods and human souls. (The other gods claim she went insane, but then, we only have their side of the story, and most of them don't come across as the most trustworthy types.) One result of this is that, with Heaven closed, all human souls now go to Hell instead. (Apart from some that end up in even worse places.) This has unfortunate consequences when people figure out that it no longer matters whether they were good or evil in life...
Garth Nix's Keys to the Kingdom heptalogy features a multiverse missing its deity, The Architect.
Temporary variant: at the beginning of Holly Lisle's novel Hell on High, God announces he's taking his first vacation in, well, ever. Two angels take advantage of his not being around to go AWOL to Earth, so they can try to convince a demon they knew before the Fall to repent and return. At the end of the book, God comes back and reveals he was giving them an opportunity to do just that.
The Inquisitor Madderdin series by Jacek Piekara is set in an alternative medieval Christianity where Christ didn't die for our sins, but instead stepped of the Cross to punish the evil with a massacre of Jerusalem ("And give us the strength not to forgive our sinners" is part of the Our Father prayer). Even though Angels clearly exist and prayer works, at least in some ways, God himself is reportedly missing and Angels have no idea how to even look for him. Well, some of them have a very strange idea which makes the main protagonist very uncomfortable...
Inverted in Small Gods by Terry Pratchett: the Great God Om has been reduced to an angry, powerless tortoise because, of all his millions of "worshipers," only one person actually believes in him any more. Until Om finds Brutha, it's less "Have You Seen My God?" than "Have You Seen My Follower?" Small Gods also features the idea that, if the Discworld universe has a Supreme Being, it's probably best not to attract his attention.
Brutha does it, too, in a very specific way. In fact, it usually takes the form of this exchange:
Brutha: Have you seen my tortoise?
Any random character Brutha is addressing: No. But there's good eating on a tortoise ...
Something very similar to this trope happens in Reaper Man and Soul Music, in which Death goes missing, presumed...er...
Another variation in Hogfather, when the titular character goes missing thanks to the Auditors and it's up to Susan to bring him back (with a little help from grandfather Death, of course).
The main premise of Towing Jehova by James Morrow is that God's two-mile-long, naked corpse has dropped into the Atlantic.
God isn't actually missing in Good Omens, but hasn't given anyone a straight answer or direct instruction since shortly after the creation. The angels think they are carrying out the divine will, but that's left rather ambiguous.
It's described along the lines of playing poker with Him, in the dark, for infinite stakes, without knowing the rules and all the cards are blank.
And the dealer smiles all the time...
The climax largely involves the uncertainty caused in the hellish and angelic armies when someone points out the contradictions. Just as Planned (probably).
His gods were simple and understandable; Crom was their chief, and he lived on a great mountain, whence he sent forth dooms and death. It was useless to call on Crom, because he was a gloomy, savage god, and he hated weaklings. But he gave a man courage at birth, and the will and might to kill his enemies, which, in the Cimmerian's mind, was all any god should be expected to do.
Subverted; Olympus has been closed and all the gods have gone MIA on the orders of Zeus himself. However, several of the other gods thought this was foolish, and so have continued to communicate with the mortal world, abet covertly.
In The Son of Neptune he seems to have changed his mind (or bowed to the inevitability of the others meddling making the plan moot), allowing Mars to order a quest. That or his more responsible Jupiter aspect can no longer ignore the situation and knows something must be done.
In The House of Hades the impending war between the Greeks and the Romans has caused the Greek and Roman sides of the gods to fight one another, rendering most major gods incapacitated unless one of their children does something particularly spectacular.
The Church of Jesus Christ the Kidnapped from the Kurt Vonnegut novel Slapstick.
Elijah is engaged in a spirit duel with 450 priests of Baal to see whose god will answer their prayers by igniting a sacrifice that has been prepared, but not lit aflame. The priests of Baal go first, and when Baal does not answer their prayers, Elijah starts mocking them, suggesting that they should pray louder because maybe Baal is sleeping or on a journey somewhere (one of his statements is sometimes translated as Baal having a Potty Emergency). Eventually, they give up and let Elijah have his turn. To showcase YHWH's omnipotence and utterly humiliate the posers, Elijah tells his servants to dump twelve buckets of water on the bull before he prays. YHWH then sends fire down from heaven to consume the sacrifice, water and all. The God of Israel neither slumbers nor sleeps.
A straighter example also occurs when Christ is on the cross: "My God, My God, why have you forsaken me?"
In the short story "The Humanic Complex" by Ray Russell, God is not so much missing as suffering from the delusion that He is merely human. An angel is sent to Him in what amounts to a therapy session. It doesn't go well.
In Mistborn, the Terran Keepers have been actively looking for their religion and which god they worshipped for a millennium. Turns out that their god and religion was the only one that was actually real. What's more, the last Keeper actually BECOMES god.
In Siewca Wiatru (The Wind Sower) by Maja Lidia Kossakowska, God has left the Kingdom long ago, taking the Lady of the Angels, Metatron and the Seraphim with him. Between the Angel leaders hiding the truth from the heavenly populace, the Angel of Destruction going rogue and God's evil counterpart getting ready to return into existence, things go south very quickly.
When Castiel was introduced in season 4, Dean wondered where his boss was. Castiel wouldn't give a definitive answer; it turns out that's because only four angels have ever seen God, and Cas isn't one of them. So he's cagey because he simply doesn't know.
Uriel's defection comes about because he thinks that 'God isn't God anymore.' When Castiel says he still serves God, Uriel replies 'You haven't even met the man. There is no God.'
At the end of season 4, it is revealed that the angel Zachariah was actively working to get Lucifer released, so the angels could defeat Lucifer once and for all; he was pretending to do the opposite to avoid rebellion among the angels' ranks. When Dean questions how God could let this happen, Zachariah says 'God has left the building.'
In the second episode of season 5, it is revealed that while the angels don't seem to know where God is, Castiel has a plan to find Him, with Dean's help. Or, rather, the help of Dean's amulet, which, as it turns out, burns white hot in the presence of God.
Gabriel confirms that God's gone, which is one of the reasons he managed to get away with living as a demi-god/Trickster for so long. "Daddy doesn't say anything about anything."
Later in season 5 it's revealed that God is still around and currently wandering somewhere on earth. He's perfectly aware of everything that's going on, and just doesn't care, and wants Castiel and the brothers to stop looking for Him. According to Joshua, "He just doesn't feel like it's His problem."
The season five finale throws us one more twist at the end, strongly implying that Chuck, the whiny prophet with a penchant for booze and prostitutes, is actually God, and he wasn't really predicting the future so much as writing it.
The conclusion seems to be that God is around, and he does care, he just works In Mysterious Ways, such as resurrecting Castiel and saving the Winchesters in the Season 5 premiere. Though, after the end of season 5, he seems to be gone for good.
In Stephen Colbert's Christmas special he prays for a miracle and gets put on hold
Amon Amarth's song "Where Is Your God?" is essentially being told from the perspective of a Viking raider telling a Christian that his faith won't save him from being killed.
Joan Osborne's One of Us, while the Trope Namer for What If God Was One of Us?, also has heavy shades of this trope, implying that God is not up on his throne in control and running things, but merely down here wandering around anonymously with humans, out of touch with the rest of the Celestial Bureaucracy.
Played with in ''Werewolf: The Apocalypse" with Ananasa, a lieutenant of the Weaver and the creator and patron goddess of the Ananasi werespiders. Ananasa is AWOL because the Wyrm has imprisoned her in Malfeas.
In the Old World of Darkness game Demon: The Fallen, the player characters are fallen angels who've clawed their way out of Hell only to find that God and all his angels are nowhere to be found. The obvious question of "well, where did they go?" is studiously left unanswered; it's up to every individual Game Master to answer it or not as he or she likes. The final OWoD sourcebook, detailing Armageddon itself, suggests some possible answers, but they're just suggestions.
In Nomine, a Tabletop RPG where the PCs are Angels and Demons has this; God isn't actually present in the first level of a classically structured Heaven, since he left His creation for the most part to its own devices shortly after the Fall. Lucifer's first overt act of rebellion was to murder God's voice, the Metatron, leaving no clear channel of communication to the big guy. Of course, every once in a while you get a "divine intervention" which might be the secret handiwork of God, or maybe one of the Archangels. It's stated that God is still around in a higher Heaven, but it's either extremely rare or completely unheard-of for a Player Character to go up the stairs, and they don't come back.
There's also Archangel Yves, who on occasion acts as a direct conduit of communication from God, and whom it is hinted (in both text and illustration) may actually be God in disguise.
Although intending to let the War between Heaven & Hell play out largely without his direct interference, in the IN universe God has directly communicated with his angels at least twice since Lucifer's Rebellion - once, to order Dominic, Archangel of Judgement, to pardon Archangel Michael after the latter was found guilty of the sin of Pride, and once to order Uriel, Archangel of Purity, to stop the ethereal genocide he was in the progress of attempting and ascend to the Higher Heavens and report to God in person right now. (Note: Uriel hasn't been seen since that day. Anywhere.)
In addition to Yves' status as maybe-possibly the Voice of God, or God's secret avatar, Archangel Gabriel is also known to occasionally speak words of prophecy that are literally direct revelations from God. The rest of the time, Gabriel's... not exactly lucid.
In Dieu Est Mort, a French Murder Party based on In Nomine, God has disappeared and may have been murdered. The players play a group of the major Archangels and Demon Princes that have gathered to solve the murder mystery and figure out what to do with Earth. Eventually, it is revealed that God was the victim of a failed assassination attempt, and re-incarnated in Yves (one of the players) to try and find the would-be assassin without using omniscience. He must also choose a regent/successor to manage things while He is otherwise occupied (or "dead" again).
In the Tabletop GamesKULT, the Demiurge disappeared, and Astaroth is looking for him, since only his counterpart can give a meaning to his existence.
Just in case you wonder, the Demiurge created the world as a prison-illusion for humanity to keep us from realizing our own divine omnipotence. In this setting God Is Evil, and Satan is worse.
In the Forgotten Realms campaign setting of Dungeons & Dragons, the Time Of Troubles was when all the gods were kicked out of their home planes and made to walk the world as (exceedingly powerful) mortals. Not just divine magic, but all magic went wonky (as the goddess of arcane magic was AFK with the rest). A few gods died. It was a whole thing.
All gods save one, that is. One god kept his divine powers in order to keep the others out.
Though several gods turned out still missing. This includes dead ones, for whom their "heirs" answered prayers — openly or not. But also still living Waukeen, who tried to escape the locked zone (by calling an off-world deity owing her a favour) and then travel to her domain while depowered. What Could Possibly Go Wrong?? Hey, this even almost worked.
Incidentally, the whole "magic goes wonky" gave the writers a perfect excuse to give the magic system a makeover when they transitioned from first to second edition.
Gleefully played with in Warhammer 40,000, where the god of the Imperium is on life-support, the Necron gods like to eat each other (and one is batshit insane), but the Eldar really take the cake. All but three of the old Eldar pantheon were killed before or during the Fall of the Eldar; the survivors are Cegorach, the Laughing God of the Harlequins, who hides in the webway; Khaine, the god of war, shattered into pieces (which sleep in each craftworld as Avatars of Khaine), and Isha, the mother goddess, imprisoned by the Chaos God Nurgle to test his plagues on. The Eldar are also attempting to create Ynnead, a new god of death, from the souls of dead Eldar stored in the Craftworlds' Infinity Circuits, the idea being that when the very last Eldar dies, Ynnead will be strong enough to rise and defeat Slaanesh. Hopefully.
To be fair it was a crap ton of Eldar dead that made Slaanesh in the first place so the force of the rest of the Eldar might just be able to counterbalance it. Either that or it will just screw the galaxy even harder than the last time the Eldar did something major to the warp. Humanity, along with everyone else who doesn't like the idea of a trip straight to hell, would be wiped out in short order.
The two Ork gods are hinted at that they are on par with the Chaos gods, and could take them if they tried, but rarely interfere with the rest of the Warp or the universe in general because they spend all of their time fighting each other.
It's also a commonly held Eldar (and fan) theory that should the Emperor die, it will be a cataclysmic event that will result in all manner of things including: a) the Astronomican collapsing, preventing all Warp travel and isolating most of the Imperium, especially the far-flung worlds of Segmentum Ultimus to the galactic "east" of Terra, b) a warp rift even more vast than the Eye of Terror opening and engulfing Segmentum Solar, the heart of the Imperium, c) the Emperor being reborn in either corporeal form, leading to a revival of the Imperium, or in non-corporeal form in the warp, leading to him curb stomping the Chaos Gods, or d) all of the previously listed.
To an extent, this trope is applicable to the Dungeons & Dragons setting Infernum - while the existence of angels is confirmed, and the most famous First Fallen do have names of fallen angels (Lucifer and Azazel being the primary), there's no detail on who God is or what he wants. Of course, the game revolves around fighting for survival in Hell, so traveling to Earth itself isn't (usually) covered, let alone Heaven, and the Fallen Angels that are player characters don't remember a thing before actually falling. What about the First Fallen, who didn't plunge through the memory-sapping Lethe Clouds? Oh, the demons ate them centuries ago - it's how the Infernum was founded.
The "Book of the Conqueror" sourcebook actually goes into a bit more detail than that: Not only are a bunch of the First Fallen still around, hiding out in the leftover bits of the previous Creation, the First Fallen Azazel and the founder of House Astyanath actually cooperated, back in the day, to build the Machine City of Cacaphractus — which nobody now remembers was actually meant as a device to torture God! So God's existence is fairly well confirmed, it's just that the sourcebooks explicitly and intentionally leave his motivations and proper role in the cosmos vague, to provide for a Rage Against the Heavens plot if so desired.
While darklords in Ravenloft are closer to damned souls than gods, their continued presence and attention is what sustains the cohesiveness of the domains to which they are bound. Domains have faded into the Mists because their darklords have died, and when Lord Soth ceased to notice his own surroundings, in favor of some obsessive navel-gazing via Magic Mirrors, his domain of Sithicus nearly broke into fragments.
The Straighter example are the actual Gods. Flavor Outlanders (people not born in Ravenloft) feeling a sudden disconnection from their gods, though they can cast spells they can no longer talk to their deities and this causes severe crises of faith. Several Fan Theories suggest that all Clerics, Paladins, and other Divine Spellcasters are actually no longer getting their spells from their gods, but instead from the mysterious Dark Powers that rules the land, so where are the Gods when their followers are stuck in a World Half Empty?
In Exalted, the reason Ignis Divine (aka the Unconquered Sun) hasn't paid any real attention to his chosen Solars is that he's too busy playing the Games of Divinity. The canonical reason for this is that he got disgusted with their behavior when the Great Curse got out of control and crossed the Despair Event Horizon.
The Alchemical Exalted's patron Primordial Autochthon is also unavailable; in his case, it's because he's in hibernation thanks to his chronic illness.
Played with a bit. The original gods of Creation were the Primordials, also known as Titans. They were cast into a hell made of their king's body and became known as Yozi. The odd thing is that in the current setting, beings at large do not want the Primordials/Yozis to return to their posts as the world's rulers.
There's some evidence to be had that the very original religion used in Dungeons & Dragons was a form of Christianity with the serial numbers filed off, but that Gary Gygax (himself a Christian), concerned that publishing it in that manner might open the game to charges of accidental blasphemy, declined to offer much of anything in the way of a cosmology at first — actual details of a cleric's god(s) were left up to to individual Game Masters. This changed later, once the Greyhawk setting was published (and by this time a pantheon had organically grown in Gygax's home campaign anyway).
This appears to be the case in the newest Magic: The Gathering setting, Innistrad. The closest thing the people of Innistrad have to a goddess, the archangel Avacyn, seems to be missing and since she was the only thing keeping the local Vampires and Werewolves and other supernatural nasties in check, the entire Plane is going downhill pretty rapidly. Her Priests are trying to keep up the slack but its a losing battle.
In the Valdorian Age setting for Fantasy Hero, the earth's level of ambient magic has fallen past the point required for gods to even exist. The problem is, people generally remember a time when the gods not only existed, but their priests had fantastic powers. Now that the priests have lost those powers, most people believe the gods have "turned their backs" on humanity in response to some horrific sin on mankind's part.
In the Eberron setting for Dungeons & Dragons, the Sovereign Host and Dark Six compose one of the largest and oldest extant faiths in Khorvaire, and maybe the world. Nobody knows if any of the gods is actually real, not even the angels or demons of other planes. The more philosophical believers treat it as a form of pantheism and dismiss the necessity of physical incarnation for a god to be meaningfully "real."
In Eberron, divine magic works on a "clap your hands if you believe" basis. There's at least one cult that is attempting to get around the problem of whether or not their god exists by building him.
And yet another D&D setting: in Dark Sun, the gods are gone (killed off or left when the world went to hell) and clerics essentially don't exist. A couple of the Sorcerer-Kings claim to be gods, and have the power to enforce their worship in their own city-states.
The play (and miniseries) Angels In America. God abandons Heaven on the day of 1906 San Francisco earthquake, and the angels are all convinced it's because humans are more interesting than they are. The angel of America tells Prior Walter to tell humanity to stop moving, in hopes that God will return to Heaven once humanity reaches a static state.
This is Older Than Feudalism: in Aristophanes' Peace, the gods have grown tired with the Greeks' constant warmongering and have moved away to the other end of Heaven, leaving War in charge.
Jade Empire: The reason there are so many ghosts and spirits hanging around and harassing humans is because the goddess in charge of reincarnation has vanished. Once again, not exactly her fault.
In Ōkami, sun goddess Amaterasu was killed in battle while under the guise of a wolf 100 years before the start of the game, unbeknownst to the public. She gets better, granted, but it turns out that a century-long absence of Nippon's chief deity isn't exactly a good thing when her power relies on the belief of her followers.
The first half of Lunar 2: Eternal Blue is devoted to Lucia's search for the local goddess to discuss the urgent matter of an awakening monster. Then the woman claiming to be the goddess is unmasked as a fraud. The true goddess decided that mankind no longer needed her and chose to reincarnate as a mortal, and has been dead for centuries.
The Diablo series includes a Crapsack World in which the legions of hell take over Earth while the inhabitatants of heaven don't want to interfere. This also allows an angel, Tyrael, to play an important part in the games' affairs.
Zehir's goal in one of the last missions in Heroes of Might and Magic V:Tribes of the East is to unite the Dwarves who are currently in the throes of a civil war. To do so, he needs to find their Dragon god Arkath. The irony of an atheistic wizard searching for a god is not lost on Zehir.
The Zuul from Sword of the Stars have lost their "gods" (the race of Abusive Precursors who created them) and are on a galaxy-spanning crusade to find out what happened to them. This is very much Not A Good Thing for any other species they happen to encounter on the way; the Zuul were made for the express purpose of exterminating their creators' enemies, and to the Zuul the act of genocide has become a holy purpose.
In the sequel, they will return. That'll be fun.
The Crystal Dragon Jesus element in a (somewhat)non-religious toned example: after the events of the first four games of .hack, Aura, the de facto goddess of the internet (in reality a very powerful AI capable of basically manipulating the entire networks) disappeared. The execs of CC Corp, the makers of The World (an in-universe fictional best-selling MMO) wanted to have her back since her presence alone made The World into such an advanced piece of software. To that end, they tried to summon her back using by the Restore Aura plan. Needless to say, it didn't quite work, and the catastrophic result actually forced them to completely close service to The World. Cut to GU era, and she's still missing. You do find her eventually, but by then, she wished for all humans to make do without an intervening hand of a deity, considering she's a danger magnet of sorts.
According to the Chantry of Dragon Age, the Maker abandoned humanity out of disgust when a group of mages tried to take over Heaven by force. Plus there was the whole "burning his mortal wife to death" thing. They worship the Maker in the hopes that if He ever comes back, He'll reward the suck-ups, but when someone like Leliana expresses a belief that the Maker hasn't abandoned His children and instead works In Mysterious Ways, it makes her a target of derision.
Also the Dalish elves have stories that their gods, the Creators, were imprisoned by a trickster god and thus weren't able to save them from invading humans. Apparently at least some elves believe that regaining their immortality and proving they're real elves would bring their gods back.
The Elvish story about how their gods were lost and the Chantry story of how the dragon Old Gods were trapped in the earth and the source of the Darkspawn are suspiciously similar, and may be different accounts of the same event.
In the Dragon Age IIDLC "Legacy", Corypheus is visibly upset when he realizes he can't hear the voice of Dumat, the first Old God to be corrupted into an Archdemon and slain by the first Wardens, anymore.
In Tears to Tiara the supreme diety Watos apparently vanished after creating the universe, leaving the angels in charge. It's not clear if he's dead or alive or what.
The plot of Lost Magic is basically that the Creator died and left a group of seven sages in charge, but then one of those sages decided to try to take over and become as powerful as the Creator had been.
In Dragon Quest IX, when you return to the Realm of the Almighty, this comes into question. Since your main character is a Celestrian (i.e. angel), it is a bit unsettling.
In Final Fantasy XIII the Fal'Cie's desire to bring back their creator The Maker, their own death wish, and the mass human sacrifice required to make it all possible are the driving forces behind the story.
Shin Megami Tensei II played with the idea - the Four Archangels, sent to Earth to oversee the conversion of souls for the case of YHVH, steadily got more and more confused about exactly what they were supposed to be doing (and quite crazy, too). The problem is that the Shin Megami Tensei multiverse runs on Clap Your Hands If You Believe, and it really doesn't matter whose belief it is. So a Fake YHVH was born from the belief of three of four of the Archangels, a monstrously powerful puppet they made, and who they served without knowing what it was. The single exception was the Archangel Gabriel, who managed to hear the real YHVH's voice.
The Human Gods of Guild Wars have withdrawn more and more from the world since the Exodus. As of Guild Wars 2, they are all but absent, though most humans remain devoutly religious. Most believe that the Gods merely wish humanity to stand on its own.
The Five were suspiciously quiet in Nightfall when their imprisoned brother attempted to break free. Even when directly called, they claimed they would only grant their blessing, not direct aid. As Kormir realized, the Sunspears needed nothing more.
In the Fall From Heaven mod for Civilization, the Creator got decided to retire and leave the world to his angels. They promptly almost destroyed it in an argument.
In Dragon Quest VII, there was a great battle between God and the Demon Lord, and it's ambiguous who won. In the game proper, you find out that the demon lord survivednote disguised as God for a while to fake you out and, although it's clear that you are God's contingency plan, you never actually see any evidence of Him surviving. Until the bonus dungeon, where it turns out He just up and retired, feeling that humanity and the Four Elemental Spirits could handle things without Him.
The Creator of the Darksiders-universe never speaks to his creations anymore. Him/her having left this universe completely is something believed by several characters, amongst them Abbadon.
In Goats, Jon and Philip meet God, who inexplicably acts like a swishy pirate guy. Philip then suggests that he change himself into a pork chop. God does so, and Philip and Jon eat him. This ends up being a contributing factor to the state of the universe - It is destined to self-destruct pretty soon unless someone renews the warranty.
Not to mention being the least Kosher thing Jon (ostensibly Jewish) could possibly eat.
In Misfile, God is entirely absent. According to Rumisiel he set up the Celestial Depository in response to Lucifer's attempted coup d'etat to avoid that ever happening again and then disappeared. He supposedly knows about Rumisiel's actions but hasn't felt moved to intervene. At least, not yet.
Jesus Christ In The Name Of The Gun by Ethan Nicolle uses this as a kicking-off point: God isn't quite as omnipresent as the Bible would have us believe. Instead, he only swings by every couple of centuries or so to see how things are going, then wanders off to leave his son to watch all this nasty shit go down. Jesus eventually gets fed up with this lasseiz-faire attitude and Second Comings a few years after the turn of the 20th century so he'll be a grown man in time for World War II and punch the shit out of some Nazis.
Slightly Damned has a interesting case, as both Gaia and Syndel (two of the three major gods) are mysteriously absent. The third god, Death, is still around though. Except that's not actually Death, but instead the rogue angel Darius Elexion, who is acting in Death's role. Death himself vanished after leaving to search for Gaia and Syndel.
We can probably imagine that this is how most of the world regarded the Avatar's disappearance in Avatar: The Last Airbender; he is the physical incarnation of the World Spirit, the lone master of all four elements and link to the spirit world. And then he disappears, an entire nation gets wiped out in genocide and war rules the world for one-hundred years.
On a smaller level in The Legend of Korra, when Aang was alive, Republic City was mostly harmonious. Yes, there were gangs around causing problems but life between benders and non-benders wasn't that bad. In the 17 years after his death, the bending-gangs are exerting more power over non-benders, even amounting to killing the wife of a prominent citizen and the gang is still running around, the ruling council no longer has any non-benders on it, they do nothing to try and quell the rising distress of the poor non-bending population, they allow bending corruption to fill Pro-Bending, the police don't seem to have any non-benders working the streets leaving no one for the poor non-benders to talk to and hope for help from, thus making the city ripe for the extremist group the Equalists to come in and slowly take over the city.
Deism is the belief that God set the universe in motion and now watches over it but does not intervene (or interfere) in daily events. A variation, Pandeism has God cease to exist (at least for a while) by actually becoming the universe.