In Super Paper Mario, Count Bleck's goal is to destroy all dimensions (Including Heaven (the "Overthere") and Hell (the "Underwhere")) by sucking them into an interdimensional black hole called The Void, and successfully does so to one. When revisited, the remnants are very different from most examples of this trope: the dimension is completely blank, save for a straight line indicating the ground and the occasional black outline of a pile of rubble; there are no survivors. Dark stuff, for a Mario game.
Although the world of Skies of Arcadia is set during an age of exploration, similar to the era of when Spain had numerous colonies, it is technically set way after the end - that is, after the Rains of Destruction fell and destroyed what the characters refer to in-game as the Old World, which was said a technological utopia until the events leading to the rains. Society has long evolved again since then, and it's found later that the only remains of the Old World that are left, along with the Gigas, is Fina's home, the Great Silver Shrine. Said shrine hosts the very elders that called down the rains in the first place...
In Fire Emblem Awakening, there is a series of DLC chapters called "The Future Past", which take place in a world in which Grima is revived and has all but destroyed the world, leaving Chrom's army to help the few remaining survivors put a stop to all of the carnage. This world is shown to be nearly identical to the main game's future, in which Grima is also revived and from where Lucina and the future children came from; their goal being to prevent that future from happening again.
The Alliance has it rough as the Horde invades Northshire and Elwynn Forest while Orgrimmar is subjected to Fantastic Racism as most of the non-Orc residents are forced to live in slums or leave entirely.
This is actually the second time that Azeroth had an After the End scenario. Ten-thousand years ago, the Well of Eternity imploded, causing the sole continent to split into what there is today. It's noted in one of the Expanded Universe novels that the event happened so quickly that the heroes barely made it to safety. While it wasn't seen, we can pretty easily conclude that hundreds of thousands died - certainly, most of the night elf empire was completely obliterated.
Third time when you include the civilizations ruled by the Old Gods. Azeroth was originally ruled by the Old Gods and populated by their various servant races, such as the elementals, Mantid, and Qiraji. The Titans destroyed this world order, killing or imprisoning the Old Gods and reducing their servant races to shadows of what they were. While the new world is friendlier for mortal races, it was definitely an apocalypse for the world's original inhabitants.
Azeroth actually had it relatively easy. After the Orcs were corrupted by the Burning Legion Draenor began slowly dying due to demonic corruption and Gul'dan shattering the links between the elements and the Orcs. Ner'zhul created a massive number of portals for the Horde to escape through, with the resulting release of magic tearing the entire world apart. The Outlands is all that remains of Draenor, a shattered continent floating in the Nether.
Doom, Doom II and Final Doom all take place with practically every other human on whichever chosen planet the game takes place on dead before you even start moving. Although in Doom II you return the favor and totally trash Hell after killing nearly every demon still in it.
Half-Life 2 takes place twenty years after an alien invasion of Earth and revolves about a human resistance fighting the against the occupation. When the G-Man takes Freeman out of stasis and releases him out into the world again, the words he sends him off with are: "So wake up, Mister Freeman. Wake up and... smell the ashes."
One of the more obvious signs that things aren't as they should be is whenever you find a dock - the water line is clearly quite a few meters lower than it should be.
The Fallout series takes place in a world that's been ravaged by global thermo-nuclear war. Most of the world is a desolate wasteland, and of the few places that haven't been destroyed most are either highly toxic, radioactive, or inhabited by the worst scum of humanity.
However unlike a lot of apocalyptic stories which end before civilization starts to get back up on its feet, the world in Fallout slowly gets better with each game and by the time of Fallout: New Vegas (204 years After the End) nearly all things mention above is gone (to an extent, or at least around what was California), and a lot of the former United States appears to be occupied by tribes, settlements (both friendly and unfriendly), and at least one known (sizable) nation.
Though the New Vegas area had a head start, being saved from the worst of the nukes by Mr. House.
Borderlands and its sequel's world, Pandora, seems to have had an After the End scenario. Subverted- it's assumed that it's never had a beginning or middle at all. Though, technically not subverted in that the human population that lives on Pandora dwindled and grew increasingly primal.
Pandora itself is simply a Death World filled with incredibly omnivorous creatures. The local bandit population are a mix of off-world convicts and former employees of the Dahl corporation that were left stranded after Dahl withdrew from the planet. In this case, it's less an After The End situation as it is simply just a shitty place to live.
Life on Pandora is miserable, but it's assumed that most of the other planets settled by humans are relatively decent places to live.
Its prequel, The House of the Dead 4, is set during said collapse; the town you're in is completely abandoned save for a Zombie Apocalypse, and it's implied that the rest of the world has fallen into this condition as well.
In Final Fantasy III the whole game starts After the End. The entire world is flooded and in some sort of stasis except for the Floating Continent where the heroes live.
The second half of Final Fantasy VI, which completely alters the world map and jumps forward a year in time... and having one of the most depressing 2D cinematics of all time. And technically, Final Fantasy VI goes through this twice: the War of the Magi, set long before the start of the game, ripped the world apart so badly it took mankind 1,000 years just to rediscover steam power.
There's an argument for the entire Final Fantasy X universe being set "after the end" given Sin's historical decimation of Zanarkand and repeated decimation of any and all towns, plus the belief of the majority of Spirans that the only way to get rid of Sin is to forgo technological advancement.
The Visual NovelPlanetarian takes place in a future world that is slowly dying after a devastating war that killed off most of humanity.
The games in the Shin Megami Tensei series all take place after the end of the world, for the most part. The nuclear apocalypse occurs about a fourth of the way through the first game, when God sends Thor to nuke Japan in order to get rid of the demons.
In Megami Tensei II, the game starts around 35 years After the End after a nuclear war combined with a demonic invasion sent humanity fleeing to the bomb shelters in 199X.
Deus Ex: Invisible War takes place 20 years after the Great Collapse triggered by JC Denton, yet in that time, civilization has returned to its pre-collapse level. See Apocalypse Not.
The Game Mod for Deus Ex2027 features this in the epilogue for the Omar ending, after they nuke most of the planet.
The Mega Man timeline is complicated. Every series but the original has a point either in-series or in-backstory could be considered "the end" From a Certain Point of View, from Mega Man X and Mega Man Zero'sColony Drops, to the war that took place between them that killed the vast majority of humans and Reploids, to the End of Humanity in Mega Man Legends, a series where the MacGuffin is the last remaining sample of intact human DNA. Mega Man Star Force takes the cake for least ambiguous End in an alternate timeline found in the postgame of the second game, which is the darkest point in the metaseries.
Most of Homeworld takes place after the Burning of Kharak.
2300 A.D. in Chrono Trigger. Your objective in the game is to actually prevent the End from happening, by traveling into the past.
Happens again in 12,000 BC after the fall of Zeal. When Zeal crashed into the surface, it not only wiped out most of Zeal's own populace but also the vast majority of the "Earthbound Ones" as well. When the dust settles, all that's left of the world is about a dozen or so people and a couple of tiny little islands. Unlike the aforementioned End, there's nothing you can do to prevent this one, since it serves as a demonstration of the disastrous consequences of abusing the powers of anEldritch Abomination.
Xenogears can count, after all, Miang decided to start a nuclear holocaust so grand that thousands of years later, there are only three big cities left on the surface of the world without most modern technology.
Phantasy Star III and Phantasy Star IV do this. It's heavily disguised in III, but it becomes apparent relatively early in IV.
Phantasy Star Online did it twice. First with their homeworld starts to wither and second being the civilization that sealed Dark Falz away.
Phantasy Star Zero did it too, set on an Earth that's been thoroughly blasted by a Dark Falz-possessed supercomputer called Mother Trinity. It happened so quickly and thoroughly that the period of destruction is known simply as the Great Blank, because nobody actually knows what happened.
Etrian Odyssey is established as being one of these in the intro... but the exact nature of the world Before The End is intentionally left vague at first.
Mother 3, though you wouldn't think so until the end, when it's revealed the two small neighboring islands the game takes place on are the last inhabitable areas on earth.
Between Halo 2 and 3, the Covenant have captured and laid waste to Earth in their search for the Ark, supposedly reducing the population to about 300,000,000. And before the series started, they wiped out Reach and most other human colonies.
Sorta; it's implied (and confirmed in the novel Halo: Glasslands) that the Covenant missed a few major colonies and the Glassing isn't nearly as effected as you think (the Spartan III's are children of thse glassed worlds so making thousands of them is never a problem).
In fact in Halo 2 you can see a room dedicated to worlds the Covenant has glassed, it's number is only 76 planets (humans have hundreds of worlds).
When the Covenant inducted the Brutes, their species was living after the end of the end; they had previously achieved spaceflight twice only to bomb themselves back into the stone age each time.
The Neverwinter Nights 2 module-building community has given us the White Rose series, set in an ice-age-type post-apocalyptic world.
Exmortis 2 is all about this: after the war between the human race and the Exmortis, the Earth has been reduced to a barren desert, inhabited only by the few humans still surviving and the Exmortis horde. For added effect, the sky has turned blood red, and the aforementioned survivors are continuously preyed upon by roaming bands of Exmortis travelling upon dark red stormclouds.
The series S.T.A.L.K.E.R. partially subverts and even inverts it. Yes, the place you're living in is a giant completely irradiated version of the western parts of Russia, but everywhere else is not only going on as usual, but completely thriving at the expense of Chernobyl by using the area as scientific research.
The prequel, Tales of Symphonia, takes place some 4000 years after a great war very much like the above one but even more damaging in its effects (at any given time 50% of the world is suffering massive resource depletion), with mankind being prevented from advancing beyond the medieval stage by a powerful theocracy (to keep them from overtaxing the limited remaining resources). The heroes fix that, even restoring the magic tree which provides the resources and destroying the theocracy - setting mankind up for the disastrous great war mentioned in Phantasia.
Primal Rage shows in its Attract Mode that the world was hit by a giant asteroid, laying waste to all civilization... and awakening a number of powerful, ancient lifeforms. They now face each other in one-on-one deathmatches in order to determine which of them will be the god of "New Urth".
Might & Magic, or at least one of the worlds visited. Enroth/Colony was a thriving, high-technological and magically developed planet before, within a hundred years, the robots of the most important control center for technology went crazy and overran it, a love drama lead to nukes being used in what was before one of the nicer areas on the planet, a massive rebellion occured against the increasingly tyrannical Governor, and a general alien invasion of the entire civilization led to the entire arm of the Galaxy being cut off from the rest of the worlds, with intrastellar infrastructure and communication being destroyed. The last is specifically cited as having caused 'a fall into barbarism and witchcraft' not only on this world, but on many others...
Heroes of Might and Magic IV starts with Enroth being destroyed by two swords of immense power clashing in battle (we even see a giant mushroom cloud). The survivors flee through mysterious portals leading to a virginal world called Axeoth, as Enroth is literally breaking apart around them. The Barbarians suffer the most, as they naturally fear anything magical, and most refuse to go through the portals. Most of the campaigns deal with the survivors building new kingdoms roughly based on the old ones. For example, the Haven campaign focuses on the new kingdom of Palaendra, populated by the survivors of the Kingdom of Erathia. They are desperately looking for any members of the royal Gryphonheart family to take the throne. That is, Lord Lysander is the one looking, while the people of Palaendra have given up and are perfectly willing to crown Lysander, who keeps refusing (naturally, he turns out to be a lost Gryphonheart heir and is forced to accept the crown).
Metroid has an interesting variant in exploring the remains of fallen alien civilisations, often finding an Apocalyptic Log of how they fell. Particularly in the Metroid Prime series.
In Legacy of Kain: Soul Reaver, Raziel is thrown into the abyss at the height of his empire's power and comes back 1,000 or 10,000 years (or more) later to find it a crumbling, decaying wasteland. Although in this case, there was no cataclysm, just a gradual downward spiral.
Super Robot Wars Alpha Gaiden Starting with chapter 10, it's a future that had, as part of it's backstory, the backstories of Xabungle, Gundam X, and ∀ Gundam, fused togther in typical SRW fashion. "Apocalyptic clusterfuck" is about the only way to truely describe it.
It's actually worse : Alpha Gaiden is set after three ends. THREE. The gravitational shockwave the heroes were trying to prevent before the time travel, a massive attack by the underground forces (aka the Dinosaur Empire and the Mycenae civilisation), and the aforementioned fusion of Gundam X's massive Colony Drop and ∀ Gundam's Black History. Wow.
In The Legend of Zelda: The Wind Waker, the entire world had been flooded, and only the Chosen people survived; the rest were killed off. The graphics are so light-hearted that it might never dawn on the player that over 90% of the population of the planet was drowned.
Chronologically long before that, we have Skyward Sword, which has the Lanayru Desert, filled with dilapidated, abandoned factories and burnt out, deactivated robot husks. Activate a timeshift stone, and you'll see them in all their mechanical, electrical, advanced glory. At the end of the game, the Hylians come down to earth from Skyloft and begin a medieval level society that lasts for hundreds, maybe thousands, of years.
Metro 2033 (and the book that it was based on) have the remnants of humanity inhabiting the Moscow metro system after a devastating nuclear war. And that's just the situation of the living, as apparently, even the afterlife was blown up.
"It appears that the devastation we brought upon ourselves was complete. Heaven, hell, and purgatory were atomised as well. So when a soul leaves the body, it has nowhere to go, and must remain here, in the metro. A harsh, but... not undeserved atonement for our sins, wouldn't you agree?"
While at first glance the setting of Inherit the Earth may look like a fantasy world of humanoid animals, the intro reveals that they became that way thanks to genetic tampering by humans, who may have been wiped out by a plague.
Resonance of Fate takes place long after humans polluted the Earth so badly that they couldn't live on it anymore due to extremely high cancer rates. The last enclave of humanity live in and around a giant air purifier built by their ancestors and have no idea the outside world exists.
This may be a stretch, but Shadow of the Colossus may apply, in a sense. Wander travels around the Forbidden Lands, which is devoid of human life, save for Wander himself. However, if one looks carefully (and does a lot of riding), traces of a prior civilization can be found, namely at the altar area in the desert that triggers the 13th colossus, and the "closed off city" that the 14th colossus resides in. Certainly not an end of all humanity or life, but an end to a civilization (maybe?), nonetheless.
The in-game setting for The World R:2 is set after a huge war where humanity kills most of the gods from R:1's backstory.
Also, the entire franchise is based on a computer virus called Pluto's Kiss destroying the Internet years before. The incident is sometimes referred to as the Twilight of the Gods.
By the time Gears of War 3 rolls around, the Locusts have destroyed the last of humanity's refuges (as seen at the end of GOW 2), the COG has been disbanded, the Lambent is running rampant, and the few remaining inhabitants of Sera are fighting for survival.
Barkley, Shut Up and Jam: Gaiden takes place in the Post-Cyberpocalypse, where the world was devastated by a Chaos Dunk performed by Charles Barkley and almost all the great basketball players were massacred in what is known as the Great B-Ball Purge.
City of Heroes: Going Rogue: The Devouring Earth has destroyed most of the earth, and mankind is slowly rebuilding. You play as a Praetorian, living under the watchful eye of Emperor Cole, whose island city of Praetoria is one of the few places where mankind can be safe.
Praetoria is in Another Dimension. Primal Earth is still (relatively) intact. This leads to some interesting problems when Emperor Cole finds out there's an inhabitable universe run by a group of people he has deemed unfit to rule themselves...
PokéPark Wii has what is possibly the most lighthearted take possible on this trope as a background element, at least as far as the park itself goes. It's unclear if humans are still around elsewhere or not.
Some interpretations of the Pokémon Mystery Dungeon games are like this, too. There are broken down human structures and most Pokemon know what a human is, but they are never seen and everyone is extremely surprised when they learn the player character is a human. Special mention goes to the Explorers games' Bad Future for being after the end of the after the last end.
In fact, some fans speculate that the main series itself takes place After The End. One theory goes that Pokemon came about due to a machine going haywire which caused a nuclear holocaust. The people that survived either remained unchanged or became the more humanoid Pokemon like Jynx, Mr. Mime and others, while the animals that survived became Pokemon. The whole theory can be read here.
Metal Walker has this, as a huge explosion turned the landscape into an unforgiving desert populated by killer robots.
Fuel takes place after environmental disasters have rendered large parts of Earth inhospitable. In addition to racing, the player character must also avoid various environmental hazards.
The Panzer Dragoon franchise pulls this off twice, as well. The series starts a thousand years after a great civilization "perished into dust". By the time Saga has rolled around, the last remnants of civilization have been pushed back a bit further thanks to the destruction of the terraforming Towers, an event known as "The Great Fall".
Enchanted Arms has this. The fact Yokohama, Kyoto and London are all in the same general 100-km radius area should give you a rough idea of how badly the Golem Wars messed up the planet's surface and layout. Despite the chaotic rearranging of the surface, Mount Fuji somehow got through the mess in one piece.
Mortal Kombat 3 has Shao Kahn destroying much of the Earthrealm, with the main characters being among the survivors of the initial harvest of souls, hunted by extermination squads who are tasked with eliminating threats to Kahn's rule.
id Software's RAGE takes place a hundred and six years after Earth was decimated by real life asteroid 99942 Apophis. The protagonist, a survivor who was put in a cryogenic time-capsule refered to as an "Ark" due to a massive international project known as "Eden Project", awakens to find Earth taken over by a tyrannic governor and finds disorder and chaos throughout the land.
Implied to be the case in Portal 2, although its unclear if the world has actually ended or if the computers running the place merely think it has, on account of the fact that the whole facility has fallen apart in the time since the events of the first game.
Dark Earth takes place a few centuries after a meteor strike leaves most of the planet in perpetual darkness from a large dust cloud. Only a few spots are relatively cloudless and allow light to shine through. It is in these spots that the survivors have built cities. Anyone who stayed behind is infected by a "dark sickness" and mutates into a monster.
The Pikmin planet, called PNF-404 in the third entry of the series, is confirmed by Word of God to be Earth in 250 million years, long after humanity has gone extinct.
Gyossait takes place after worldwide natural cataclysms caused by the titular goddess of Earth. What's left of humanity lives in small tribes in ruined buildings, trying to survive the progressively harsher climate, mutant attacks, and the defeated goddess's eldritch powers.
Anarchy Reigns takes place after world war has torn the world apart and rampant industrialization by the surviving powers has polluted everything else, leading to rampant illness and mutation.
Yggdra Union has 2 examples. Lost Aries is a wasteland which is all that remains of a civilization destroyed by the Dragon of Purgatory. Near the end of the game, the setting's equivalent of Atlantis rises from the sea.
In Wizard 101 the player arrives at the worlds of Dragonspyre and Celestia after they had been destroyed by the Dragon Titan and the Storm Titan respectively. Dragonspyre looks like hell arrived in a large medieval East European city, with rivers of lava and bones littering the ground. Celestia is the equivalent of Atlantis except the Piceans and Crustateans have since found it and are beginning to build their own empire in the ruins.
Would you believe Hatoful Boyfriend has this for its backstory? To wit: Decimated by a superstrain of bird flu, humanity attempted to eradicate the plague-carrying birds with an engineered virus of their own. The birds that survived the latter developed sapience, realized humans were trying to kill them, and fought back, killing even more humans. And now you know why all the love interests are pigeons, and the human heroine lives in a cave in the middle of the wilderness.
Bastion takes place after the Calamity tore Caelondia and the surrounding area (and possibly the entire world) to pieces, leaving only four people and a small army of pissed off Ura ready to take revenge on what's left of the nation as the only known survivors.
Danganronpa is set in an environment where students are trapped for a long period of time and forced to kill each other. Why don't the police ever show up? An event happened that caused a huge worldwide conflict, and there are no police or even people to control what is happening inside the school.
Centipede: Infestation, a Centipede re-imagining for the 3DS and Wii, creates a plot for the game. It takes place in an post-apocalyptic world where only a few humans exist and there are many Big Creepy-Crawlies.
The 2013 Call of Duty entry, Ghosts, is set ten years after a cataclysmic hostile attack destroys much of US society, turning the country from a powerful global force into a shell of its former self. The government unable to afford a proper military (likely having lost too much money on the recovery effort), the eponymous "Ghosts" are called together from all remaining branches of special forces to form a single spec-ops organization.
Most Armored Core games have one or take place after one. Best examples are Last Raven which happens after the unmanned suicide weapons destroy the world in Nexus and V/Verdict Day which take place in the distant future of For Answer after the National Dismantlement War, LYNX War, the conflict with the League and ORCA and it's constant use of Kojima particles.
Seven Days To Die takes place after a Third World War. Oddly enough, Navezgane seems to be perfectly intact, aside from it being surrounded by a nuclear wasteland and the entire population withstanding of zombies.
This seems to be at least partially why the world in Gingiva is such a Mind Screw: the world has taken over and horribly twisted by some evil megacorporation for materialistic purposes, and almost everyone has been enslaved.