This is pretty much the default for much of the world in the AU, the 1983: Doomsday Stories, at least in the first 10 years or so after Doomsday. A good deal of the Nations are dead. Those who survived the initial nuclear carnage were forced to a grueling existence of simply trying to stay alive from day to day. Eventually, things do get better in some parts, like the Alpine Confederation.
The setting of Code Geass Megiddo: Japan was totally destroyed by imploding the underground reserves of sakuradite and ALL faction, including Britannia, The EU, the Middle East and Chinese resistance are all narrow-minded racists (even in the Black Knights they are present). Britannia just conquered most of the world simply because they're more efficient, but in reality you don't cheer for anyone. Lelouch's goal to destroy the world and make something new makes much more sense.
Its rewrite Aeon Entelechy Evangelion at the first glance seems to be a little lighter, what with stabilized fronts, the Rapine Storm successfully contained and with everyone being much, much more competent. And then we are introduced to the TITAN AIs, and one of them is based on CABAL.
Death Note Equestria: After centuries of being a Sugar Bowl, Equestria is completely unprepared for the increase in crime that comes with the increased population. As a result, its justice system is ridiculously inefficient, to the point of convicted murderers getting released when a prison gets overcrowded. This is what motivates Twilight Sparkle to become the first Kira and begin killing criminals.
The Infinite Loops were started when the multiverse crashed and damage was done to multiple realities. That's not this trope. What is this trope is loops that are quarantined, either due to being so full of viruses and malware they could Mind Rape any Looper that winds up in there, or simply having enough baseline power to pose a danger to the multiverse.
The State of the world in Mighty Morphin Mecha Rangers is mainly a background issue, but between Japan which is heavily implied to be heavily influenced if not controlled by CommanderIkari, the clearly untrustworthy USA that controls almost all of the Americas and Vietnam, The BritanniaEmpire which is in control of a huge portion of Eurasia, and the Earth Federation that houses both of them and several other nations...somehow living in a city controlled by Kaiba doesn't sound so bad in comparison.
In Project Ignition it sucks to be on the Earth. It really, really does. Starting back in the 1970s, there's been an Alien Invasion (it left the world to be as described "That fucked up world"), constant warfare where civilians often ARE the targets, and if you're not getting killed by some corporate, you're living in slave like conditions, there's highly corrosive radioactive particles floating in the air, EVERYWHERE, and dying of "Kojima Poisoning" is EXTREMELY painful, and common. And oh, the aliens are back- and the best weapon to fight them? It spreads the aforementioned "Kojima Particles". Yeah, everyone is just shy of "Fucked" and "Fucked Harder". And that plan to escape the Earth? You know, the Closed Plan? Corporate Scheme.
Soul Chess: Given it's ParentSeries, this is pretty much a given; both the living world and the afterlife are pretty nasty places to be on the whole. The first part is mainly afterlife based; crime and disease are rampant, living conditions are woeful, and the nobles do pretty much what they want with impunity. Lelouch spends over a century trying to make things better, sometimes through being an All-Loving Hero, others by being a Manipulative Bastard (mainly tricking the Gotei into getting off their backsides and dealing with the problems themselves). Later actions shift to the world of the living. He knows the living world is going to get more crapsack; he's lived through it once, and now gets to see all again as a spectator. And because of the Grandfather Paradox, he knows he can do absolutely nothing about it.
The world of The Faceless an AU with a Broken Masquerade exposing the reality of the Shinigami World to the human race which results in a post-apocalyptic world of nihilism-civilization has collapsed, it's a world of permanent war, everyone wears masks and are busy Dying Like Animals.
The Odyssey. It's set in Exalted, and the protagonist is currently a mortal. That should tell you all you need to know. Every day is a constant battle for survival, pitting sheer determination against the overwhelming power of the Realm's Dragon-Blooded.
Harry Potter Fanfictions love this trope, and it doesn't even require the Voldemort to be even in a body to do it, Pureblood behavior allows the fanfiction writers to make a world that is the absolute worse way to view medieval society...and it isn't so much a crack fic as in other worlds. After all, you have people like Umbridge in power....
Faery Heroes starts off in a future where Voldemort attacked the Muggles, and ended up causing the magicals to be in desperate war of survival, with all the magicals forgetting he started it. The first chapter featured a dying Santa Claus due to how bad it was for crying out loud.
The Firebird Trilogy of stories also has a very, very well constructed Crapsack world. The fic deconstructs the harem genre in the most horrifying manner, creating a world where sexual harassment of young males is encouraged, Goblins are witch raping, iumpregnating horrors, and Voldemort (Who is very much his canon counterpart, if perhaps worse), is seen by most of the fans as a hero....and Goyle is a girl. Squick
To explain the first, if girl or woman doesn't "poach" a boy at a young age, they are likely to never get married or have a partner at all due to the extreme gender imbalance. So young teen girls have to plan out seducing, blackmailing, tricking, or outright raping a good prospective mate if they hope to have any sort of future at all (as power and success is found in family groups, rather than as individuals).
The Harem War has over a third of all magical females as concubines against their wills, hinted to be killed in later life after being made as sex slaves at very young ages, with the rest of the magical females in general being treated poorly.
Harry Potter and the Altered World has this with large conflicts in Russia, China, South American and Africa, but in a What If version of the story the world is so bad that Bellatrix teaches at Hogwarts, muggle borns can't buy books for school (this includes Hermione) and all the main characters are either orphans or abused. Not to mention that world had Voldemort as a hero to Muggle Borns and Half Bloods....and he was killed by accident by an evil James Potter.
There's a world in the realm of Fan Fiction where daring to like what you wish to can result in torture, where ideology can get you imprisoned with guards who are Mind Rape incarnate, where pedophiles are allowed to be teachers, and where you can get away scot-free for murdering someone who asked you to quiet down in the movie theater. In this world, students are tortured, reason seems to have fled, and whatever choice you make on ideology, you are doomed to become reviled, except if you fill some completely arbitrary criteria. What is this horrific world? It's My Immortal, widely considered the worst fanfic ever written.
Horseshoes and Hand Grenades is set in the optimistic world of Fourze...except in this world, Gentaro's death brought in an ancient serpent who resurrected him and now Gentaro's planning on destroying the world. Moreover, other serpents have begun possessing people who have also recently died, other Kamen Rider shows got involved in the mix, the original Big Bad is crossing lines and the Mysterious Benefactor is being amoral for some odd reason. All in all, friendship isn't going to be the shining beacon of light in this fic.
The setting of Bad Future Crusaders — the Face Heel Turned Queen Twilight Sparkle has turned conquered Equestria and the Crystal Empire, turning them into a totalitarian Police State/Empire, whose military has no problem with bombing population centers in order to drive fugitives out of hiding. Meanwhile, what we've seen of the rest of the world isn't nice either, as Sonhos Vale (the country where Apple Bloom and Silver Spoon grew up as refugees) has been split by civil war for so long no one remembers why, and Saddle Arabia has suffered from such serious drought that its society is on the verge of collapse.
The Pony POV Series has the Epilogue timeline (based on the first series' Alternate Ending, later expanded on by Applejack's glimpses in the Truth, and eventually explored in-depth by the Dark World arc), which shows what would have happened had Discord succeeded in conquering Equestria. It is possibly the ultimate Villain World, where the Mane Cast have been brainwashed into Discord's loyal enforcers, killing anyone (including children) who opposes him (and sometimes for no reason whatsoever), while at the same time are victims of his mind games the same as everypony else. Meanwhile, Discord's rewritten history to make himself seem benevolent compared to the deposed Celestia and Luna, even as he causes random chaotic events on a daily basis for his amusement — among other things, it seems the dead rising to eat their loved ones is a common occurrence under his reign. Need I go on? It's such a horrible place that even Original Timeline!Discord is unnerved by it.
Ironically, when we return during the Dark World Arc, part of the story is showing that there's still good in it, including the previously mentioned Sea Ponies, griffins and pegasi giving up racial tensions and essentially merging into one species (hippogriffs), and Changelings have gone from parasitic love vampires to downright heroic. While its still a nasty place to live, there's at least hope of saving it. And a redeemed Twilight is going to try.
The Alternate Universe depicted in Sunshine And Fire. It is not at all a pleasant world - the Endless Daytime brought on by DaymareSun has caused water (and thus the ability to grow crops) to become a luxury with death by dehydration a very common occurrence, the Earth Ponies being horribly treated and discriminated against, children are taken away from their homes if they have a special talent that could be useful to the Queen (and they're often Brainwashed into her ruthless agents on top of that), there's political infighting, murders, reeducation, and treason both direct and indirect.
With a world filled with 9 ultra destructive demons who have a habit of escaping their human prisons and people capable of causing earthquakes, summoning snakes big enough to eat cars, mind rape people and in general causing mass destruction, Naruto worlds are rarely that far behind the Harry Potters.
You know how Treasure Town in Pokémon Mystery Dungeon is listed as one of these? In Brave New World it's about eleven zillion times worse. The entire town is built upon a huge gate that contains the most evil thin in the Omniverse (that is, a collection of every multiverse ever), and it is the primary base of the Nhilators, a villainous group that at times gives Chaos a run for it's money. There is exactly one character from Treasure Town that is not evil, and he's a ghost who became a priest in order to repent.
Also there's a place which is worse than Treasure town... Genocide city, a place worst than the gate to hell... Well, treasure town is soon worst than it, but still just what could have happened to make a place that bad?
The entire world in Poké Wars has become one of these, what with wild 'mons running rampant in a discoordinate, but efficient, effort to wipe humanity off the map. Cities covered by Muk sludge, towns overrun by Fearows, legendaries practically nuking large settlements... you get the idea. It's even worse when you find out that the Pokémon's powers were amplified way above their original levels. Johto got it particularly bad, being the "rebel" Pokémon's main stronghold.
The Sun Soul, a story set in the Pokémon universe is essentially a highly methodical deconstruction of how brutal and dangerous a world with such monsters would be. A single Gyarados for example is more than capable of wiping a small town off the map. The villians start and control wars from the shadows, orchestrate crises to further theit political power, and merrily murder anyone who gets in their way. The heroes are, of course, trying to fix all this but in a world stalked by one horrifyingly effective Hero Killer after another, where being Killed Off for Real at any moment is a real threat, it isn't easy.
And if the preview is any indication, the sequel takes it up to roughly eleven billion. The Forerunners return, destroying a good chunk of the entire universe. The Demon Empire and Angel Federation promptly collapse and many of the characters are either dying or implied to be dead in the very first chapter.
The Shape of the Nightmare to Come - Dark Fic of Warhammer 40,000, the patron saint of all crapsack worlds and turns it's crappiness Up to Eleven. The God Emperor of Mankind dies and is reborn in the Warp as the Star Father, ruthless Chaos God of Order, the Astronomicon collapses, so the Imperium of Man gets fractured into several smaller empires, out of which many are even worse than it was and most of its' forces are either destroyed or start mad, fanatical crusades. The Tau turns into bitter conquerors who sees other races as lesser ones. Most of the Eldar die to awake Ynnead, who ends up trapped in the Infinity Circuits so they all died for nothing. Chaos breaks from the Eye of Terror and two Chaos Empires - one ruled by Abbadon and another by Huron Blackheart - rise. The Orks and Tyranids merge into terrible New Devourer that eats half of the galaxy. The Void Dragon breaks free through ends trapped in Sol System. Oh, and the Necrons have unleashed Ophilim Kiasoz, an Eldritch Abomination that unmakes solar systems just by passing through them. The introduction sums it up:
It is the 51st Millennium and I cannot wake up from this nightmare! I cannot wake up!
It's sequel, The Age Of Dusk, may be heading into that direction - while some things gets better, many gets much worse.
Re: Yin Yang Who? has one of this story's review summing it up as this... partially.note ->"Angst, Tragedy. Dreams shattered by a single word of denial. Fear overwhelming a sense of justice. Because of a single twist, lives were changed drastically, loved ones were lost, and a crueler environment rose up. With nothing left but painful memories of the former lives they lost, the warriors continue on living in their new home."