Violence Jack by Go Nagai is perhaps the first post-apocalyptic anime/manga. The series is set in the chaos after a massive earthquake and volcanic eruption leveled Japan and focuses on the survivors of the Kanto region, who are divided between the strong and the weak. It's noted for its over-the-top violence and brutality, and would serve as the inspiration for many violent anime and manga to come.
AKIRA is set in the aftermath of the destruction of Tokyo. It starts out fairly cyberpunkish, but soon moves full into this territory.
Neo Human Casshern takes place in a time when Androids have taken over and a man who placed his mind in a superior android fight back against the androids with the help of his dog, Friender.
The series Casshern Sins that aired well over thirty years after the original is after the end — of the end, as now the androids society that conquered humanity is crumbling because of a disaster caused by this version of Casshern, who lost his memories and wanders the ruined Earth searching for answers to questions he doesn't know.
And the 2004 live action movie adaption: Casshern.
Ergo Proxy takes place after a "detonation of the methyl hydrate layer", and as a consequence, the remains of humanity live in giant domes protecting them from the outside world. Said calamity may or may not have been the direct result of nuclear war. Rapture looks suspiciously like those pillars of flame showing during end of the world flashbacks.
Luckily the original human inhabitants saw it coming, or at least responded in time and fled into space, leaving the Proxies behind to rebuild civilization. It didn't turn out very well.
Fist of the North Star is set in 199X, where the earth has been devastated by nuclear war and nearly all living things have gone extinct. Evil warlords and vicious gangs roam the land, killing and subjugating the weak. Thankfully, there are heroes ready to defend the people and make these villains pay, several of whom are Badasses with a mastery of a mysterious but horrifying Pressure Point based martial art.
To a lesser degree (in that only about half of humanity is gone), Neon Genesis Evangelion. The goal of the protagonists is ostensibly to stop various people and things from finishing the job. Ostensibly.
In a meta-example, Hideaki Anno actually made a parody radio drama together with the main voice cast after The End of Evangelion. It was called "After the End", and in it the characters discussed what they would do for a sequel now that everything had gone to hell. It was kind of Anno's own version of the now-famous Spike Spencer "Shinji Rant". All of that joking about a sequel isn't so funny now, is it?
This happens for real in Rebuild of Evangelion 3.0., which takes place 14 years after 2.0., where the Third Impact that occurred there wiped out most of humanity and apparently ravaged the planet even worse.
Robotech, Super Dimension Fortress Macross, and Genesis Climber Mospeada - In Macross especially, where the remnants of humanity and Zentradi eventually manage to rebuild civilization after the planet suffered nuking. Macross City is the capital, built around the SDF-1, with homes, shops, schools and offices, and situated in a barren Alaska, with other cities miles away (possibly around Canada and some of the USA, although it's not specified where each city is located). The creators of the franchise eventually wanted to show a much cheerier image of the post-apocalypse after the big victory, however, the capture of a Zentradi satellite factory helps humanity to colonize the stars, meaning that there is a happy ending for most.
Vampire Hunter D. After two ends, no less. First a nuclear war late in the 20th century or early in the 21st that reduced humanity back to the Medieval era, and the slow hubris of the vampire super civilization that followed five thousand years later, and lasted another five thousand years before the humans were truly back in charge, yet still underdogs in the distant frontiers.
Part of Kurozuka takes place after the world has been devastated by unintentional nuclear holocaust (the nuclear powers were trying to destroy an asteroid, but accidentally targeted each other instead) and the resulting nuclear winter.
Hyper Police — the apocalypse brought most fantasy creatures to Earth (gods, oni, beastpeople including werewolves), and left humanity as a protected, endangered species.
Overman King Gainer has the cast believing that the Earth has healed from mankind's presence, and trying to reach Yapan, the home of their ancestors, from Siberia where a good portion of humanity went to live in Domes.
Tsubasa Reservoir Chronicle, in Acid Tokyo, a Tokyo destroyed by acid rain where the survivors protect the eponymous reservoir, and, consequentially, Clow.
Played with when it's revealed that Acid Tokyo is the ancient past of Clow Country. Those ruins Syaoran was investigating at the beginning are the remains of the city's buildings.
Getter Robo Armageddon as well as the Hien and Ä€ḥ installments of the manga.
The manga 7 Seeds takes place after an devastating asteroid impact event destroyed human civilization and dramatically altered the environment. The only remaining humans on Earth are selected teenagers (and adult guides) who were frozen shortly before the apocalypse.
Trigun: An interesting variation. Turns out the current state of affairs came to be after humans ruined earth and then escaped into the universe. Then some drama happens among the crew, resulting in millions of people dying and the remainder being haphazardly dumped on the planet where the story is set.
Rave Master. Technically, the world the story is set in is a parallel world created by the last surviving human after famine drought and plague destroyed the original world. The main villain, the only descendant of that sole survivor and, therefore, the only 'real' person, wants to go back to that world.
Possibly Naruto. Between the severe levels of schizo tech, the bizarre structures in Rain country, and the wreckage that the Uchiha weapons stash appears to be located below, it's never been explicitly stated but it would explain a lot. The probable source of said apocalyptic event is most likely the Juubi. The wreckage in particular has an after the end feel to it.
In EL, the Megaro Earth Project is implied to be the last remaining city populated by humans after nuclear war devastated the Earth. At the end of the second OVA, it is revealed that the situation is far worse as only El and a single human male have survived, kept in a coma-like state by sentient AI hoping to find a way to breed them.
Wolfs Rain, though it is not initially clear, it is shown that the world is in the middle of a nuclear winter, and the few cities and towns huddled in domes that we see are one of the only bastions of humanity left.
In the backstory of The Mysterious Cities of Gold, Mu and Atlantis fought a nuclear war that wiped out both empires (as well as most of the rest of humanity) and almost all of their uber technology.
Sky Girls Although everything LOOKS nice and neet and clean it takes place after an alien invasion that has killed off nearly every man on Earth leaving girls to defend Earth should there be a second invasion. Possibly only 1 out of every 100 people left is male.
In Dragon Ball Z, Future Trunks' timeline is this thanks to a pair of rampaging androids and why he comes to the main timeline to prevent it from happening there.
Sonic The Hedgehog The Movie: the strange fantasy world in this movie appears to be this, but it's never really explained. The creatures of this world appear to have rebuilt society and moved on... or they just don't mind abandoning tall infrastructures and New York City sized settlements.
Psyren is about a group of people that are being sent back and forth to what remained of Earth after the cataclysm that wiped out most of the existing lifeforms and transformed the surviving ones into dangerous mutants.
The world of Toriko was ravaged by war in the past. Then the legendary chef Acacia invited the world leaders to a full-course meal consisting of ingredients from the Gourmet World. After eating the main course called "GOD", the world leaders experienced enlightenment and worked together to bring about peace.
The world of the Monster Rancher anime is explicitly stated to be this. The human civilization which created the monsters was crippled by natural disasters, then the survivors fought an increasingly destructive war until Moo was created to be the ultimate weapon, except he decided to just destroy everything instead. The last few survivors barely managed to create the Phoenix and defeat Moo. By the time the series takes place, civilization has returned to a Medieval level with occasional Schizo Tech.
Megazone 23: Long ago, the Earth's climate collapsed under the weight of humanity's abuse. Humanity left in generational ships, of which only one survived to return.
The Big O is set in a city which was built after an unknown event caused mass total amnesia. Everything else is believed to be barely-inhabited wasteland.
Attack on Titan is set in an unspecified future where humanity has been reduced to a handful of walled villages that are constantly under threat from roving giants that seek to eat them alive. The story follows the main defense force of the last city on earth as they seek to take the fight back to the monstrous Titans.
Magic Knight Rayearth in the second half of the story, due to the death of the Pillar. Everyone in the country has been moved into a tiny castle surrounded by crumbling wasteland being eyed by foreign invaders.
In Neppu Kairiku Bushiroad, a poison later known as "Shinobi" came to our world from space, after which despair took over, with the people being driven to a place known as "Kairiku". The only things left that can save humanity are a mysterious human weapon by the name of "Yagyu", and the holy weapon "Giga Road".
In Kill la Kill, an as of yet unspecified disaster has caused almost all of civilization to completely collapse. Only a handful of cities remain habitable, one of which is (of course) Tokyo, which has become a facist police state.