TexhnolyzeThose living on the surface are little more than shades of humans who live without purpose. The underground Lux is thrust into slaughter and carnage in the last few episodes, with essentially everyone dead by the end as the city goes dark.
Utawarerumono It is implied that this is the real setting of the story. Humanity has either departed the planet or is plain old extinct. The half-human hybrids populating the planet are genetic creations of humanity.
The truth is far more sinister. Hakuoro turned the remaining humans (most have died in an implied cataclysmic war) into blob monsters, although to be fair they killed and dissected his wife and child first.
Atavar takes place in a future where humanity is extinct, having left behind a race of robots called UOS. UOS is bent on wiping out all life in the galaxy. Nice going, humans.
There is a Teenage Mutant Ninja Turtlesone-shot that deals with this topic. The Mutagen that has been used so copiusly by villains and corporations alike has leaked into the groundwater, and all children, be it animal or human, born from this point on will be mutants. The story deals with Michellangelo's pondering on the fact that he and his fellow mutants will be the ones to inherit the Earth when humanity finally goes extinct.
Although the movie never specifies one way or the other, it is implied (especially by the circuitry seen through their bodies) that these humanoid beings are not aliens, but robots like David. They are either the last creations of the extinct human species or of their own predecessors (robots building more sophisticated robots).
This is foreshadowed by Giggolo Joe who explains why humans fear robots.
The so-called aliens are clearly the latter, as they state in the movie that David and Teddy "knew living people", implying that the robots there never met humans (except for the ones they brought back).
Omega Doom: In this B-Movie, humans are dead, robots inherit the Earth... and rule it badly, having devolved into an Enemy Civil War. Except there's one last enclave of humans, and they're out to clean up the bad robots by sending out the reprogrammed protagonist.
Rock and Rule depicts the humanoid descendants of dogs, cats, and rats (along with the occasional mutant) living atop and amongst the ruins of human civilization. They seem to have recreated a fairly accurate simulacrum of late '70s/early '80s North America.
There was a short story by Arthur C. Clarke about alien lifeforms from Venus studying the few remaining artifacts of the human found on a frozen Earth. The one that confuses them the most is a short film portraying people behaving in a variety of strange ways, revealed at the end to be a Walt Disney cartoon.
The book Re Body, Robots kill us all, revive a human head, and set out to destroy some uplifted animals we had created.
Many H.P. Lovecraft stories don't take place in such a setting but have the idea of humans as an insignificant blip in a universe of monsters about to be snuffed out. Mike Mignola's works also have visions of a future-earth where man is no more.
The Shadow out of Time explicitly states that at least 14,000 years in the future humanity will die out and be replaced by a race of intelligent beetles (into whom the Great Race of Yith transfer their consciousnesses).
Lovecraft takes the theme in a different direction in Memory, where a demon and genie idly contemplate a number of apes. One eventually remembers that the apes are the descendants of an older race called "man."
"The Stainless Steel Leech" from the story collection Last Defender of Camelot, in which humanity has died out, leaving behind a society of robots. They've adopted the behavior of humans for the most part, though developed strange superstitions. One of the robots developed a hardware problem and became a vampire of sorts, and while hiding from the rest came upon a human vampire, the last of its kind and slowly starving from lack of blood.
"For A Breath I Tarry" from the same collection has a similar setting, used as a retelling of Faust, though the tragic ending is averted by the creation of a new race of humans.
In Requiem, it is mentioned that once humanity finally managed to wipe itself out, two factions arose, each seeing itself as the true descendants of mankind: the robots and the mutants. The robots are animalistic tanks (elephant, gorilla, TRex...) while the mutants are hybrids and zombie-like things.
Brian Aldiss's short story But Who Can Replace A Man? The robots are overjoyed that humanity is wiped out and they are now free, but they end up nuking each other and in the end they come across one surviving human, whom their programming compels them to obey.
Dougal Dixon has written two versions of this trope. In After Man, the Earth is repopulated by descendants of the small animals (like rats and rabbits) which an extinct humanity failed to take down with us. In Man After Man, humans speciate into dozens of varieties, some sapient but most not, through a combination of genetic engineering and natural selection.
Last and First Men by Olaf Stapledon has all of the "First Men" killed in an atomic holocaust 100,000 years from now. Save for thirty-five who mutate into the Second Men, starting a cycle of extinction and replacement that continues for two billion years and 16 more species until the Eighteenth Men die when the Sun goes supernova.
The short story Written on the Wind by David Levine, has a federation of alien races trying to decipher a message coded into the fabric of the universe, which turns out to be from humanity who destroyed the universe through nanotechnology; before the end they were able to program the nanites to rebuild the universe and create new and more diverse life.
In short story "Pots" by C. J. Cherryh a race of aliens comes across a space probe with Pioneer plaque on the board, after mankind is long gone from the Earth. They attempt to find remaining descendants of humanity, while spreading romantic legend about first space travelers across galaxy. They remake their whole social structure, with hibernation and Cloning Blues for top leaders and scientists, for this purpose. When group of archeologists finally finds something on third planet of small, yellow star it turns out humankind destroyed itself shortly after setting foot on the Moon.
There's also a short story (whose name and author I can't remember) that basically does the same, but with an automated bomber jet. It is implied that it nuked the remains of that one city for a few ten thousand times.
When taken in the context of The Martian Chronicles where it's reprinted as part of the setting, the smart house has only been going through the motions for a few days at the most after World War Three (it still has fresh bacon and eggs to make the uneaten breakfasts with, and the master's dog is still barely alive). Though humanity hasn't been wiped out completely, human civilization has essentially suffered the same fate as that of the Martian's, dead and remembered only by those few survivors (Human or Martian) left.
This is the central premise of The World Without Us. The book is a thought experiment by Alan Wiesman on how our infrastructure would crumble and fade if humanity were to disappear entirely.
In Angel Notes, the human race has genetic-engineered itself into around a hundred different sub-species that, collectively, refer to themselves as the human race. The main character is the final remaining true human being, and he dies at the end. This is not good for the human race, as only a true human can use the Black Barrel, one of the only effective weapons they had against the invading Aristoteles that desire to annihilate the remnants of humanity.
Live Action TV
One episode of The Outer Limits 90's series had robots try to resurrect humanity, and in another, aliens.
In the new series of Doctor Who episode, set billions of the years in the future, "The End of the World" Cassandra claims to be the last human. The sequel story ignored this and offered a HandWave to the effect that there are billions of mutants and hybrids (most of whom look exactly like H. sapiens) and she's just a racist. A latter story "Utopia" showed humans existing 100 trillion(!) years from now. (Humanity has come back into existence in the meantime, handwaved by the Doctor saying that even though humans humans did go through different evolutionary forms, they always seem to return to their basic form eventually.)
Red Dwarf takes place millions of years after humanity's extinction, apart from Lister who was in stasis for a very long time.
The Future Is Wild describes many animal species that evolve long after humanity has left the planet. In the last segment, a new type of tree-dwelling cephalopods show signs they may develop a civilization of their own.
The book the documentary is based on plays this totally straight, with humanity having died out.
Finally, robotic beings rule the world The humans are dead.
"Fairy's Paradise" by Coco Rosie is about how after humanity nukes itself out of existence, the fairies will frolic in the ruins of our civilization.
Occurs in the Time Skip between Mega Man ZX and Mega Man Legends. Humanity managed first combined with reploids to become superior cyborgs, then created organic robots in the image of what humans used to be like as a servant race, then true humanity goes extinct, leaving the servant race behind to try and fend off the fail-safes that now think they've Turned Against Their Masters. The series MacGuffin of Legends is the last remaining sample of human DNA.
NieR: The events of the game ensure that the remnants of humanity will die out in a generation, as Gestalts can no longer prolong their descent to madness and Replicants cannot reproduce.
In Furthia High humans turned themselves into furries at least a couple generations ago, Kale is the last known human.
The big reveal at the end of thisSaturday Morning Breakfast Cereal comic is that the astronauts in the pictures are aliens landing on a barren dead earth and reading a monolith left behind by humanity describing how they gradually moved into virtual reality where the perception of time was greatly accelerated.
Dear traveler: please don't think ill of us. We are the last generation. And we are immortal.
Technically averted in the Orion's Arm setting. True members of Homo sapiens sapiens still exist in large numbers, but they are rare in comparison to the overall population of humanity's descendants and are generally only found in baseline reserves.
In The Periodic Table Of Science Fiction, one of the stories features a miner who, waiting for a rescue ship and with nothing to do, uses the harvested ores to paint the surface of the asteroid he's stranded on. It eventually becomes acclaimed an artistic masterpiece and a galactic cultural treasure by alien species long after the human race itself disappears.
Day Of The Barney Trilogy has Barney temporarily succeed in creating a society that, had it existed long enough, would have resulted in this. After the Great Act of Love, every adult and teenager hides from Barney and his followers while every human child has become Barney's Special Friend. Barney cares for them and makes sure they're well-fed and happy until they turn thirteen, at which point he murders the boys and takes the girls away so he can rape them and impregnate them with Loved Ones. Due to the allure of Barney and the inclusiveness of his group of Special Friends, as well as the combination of boys generally not being able to reproduce before reaching the age of thirteen as well as them (hopefully) not performing sexual activity with the girls, the full-blooded human race would have died off if Barney had reigned for long enough, with the Loved Ones as the last surviving remnant of humanity.
There was an episode of Super Friends in which aliens find Earth devastated and lifeless. They search our records, find that one of the Legion of Doom's schemes had terrible unintended consequences, and used time travel to set things right without making their intervention too obvious.
Similar to the above, one episode of Justice League Unlimited had Superman catapulted into the future thousands of years by a so-called disintegration ray, where he discovered Vandal Savage had inadvertently wiped out the rest of humanity in one of his attempts at world domination. As the only sentient being on Earth, he went insane, grew Bored With Insanity, and then invited Superman home for dinner. "Like you've got anything better to do."