Bicycle Boy takes place in a post-apocalyptic desert, though it is unclear where on earth.
Blade of Toshubi is set on a future Earth where the only humans survive in arks orbiting Earth while animals have been artificially 'evolved' into sentient bipeds.
Bubble Wrap - where most of humanity was wiped out due to a contagious virus. The surviving humans don't have to wear protective suits at all times...unless they have an aversion to dying, in which case it's a good idea to stay dressed.
C 0 DA - The sequel to The Elder Scrolls series by longtime series mainstay Michael Kirkbride (with support from current Bethesda writer Kurt Kuhlmann). Numidium has made Landfall. The Thalmor won, time is unbound, Nirn is uninhabitable and the survivors eke out a living under the surface of the moon. Humans are ambiguously extinct, as the only races seen in the comic outside of flashbacks are Dunmer, Khajiit and Hist.
Circa After The Apocalypse takes place after an undetermined time period after Earth is bombarded by meteors, which devastate the world and raise a dust cloud that blots out the sun- the dust cloud seems to have settled prior to the events of the comic itself.
Cthulhu Slippers is set after the end of the world as we know it after an invasion of all powerful alien gods. That the gods are dumber than a bag of hair is beside the point.
The Demon Archives is set on Earth about 100 years after nuclear and biological war destroy global civilization. A few high-tech organizations were prepared, survived the nuclear winter and actively work to re-establish civilization on the war-torn Earth.
Derelict A mysterious event has flooded much of the world and turned many humans into misshapen monstrosities; roaming scavenger Deng attempts to stay alive and keep her small boat fueled.
The world's been "broken" four times in The Dragon Doctors. Once in a war between evil puppet masters and upstart magic users, a nuclear war, a meteor impact, and a disaster called "The Dimension Fusion" that mixed up parts of Earth with parts of other dimensions. Each time started a new calendar.
Drowtales is technically set after two ends: the first was a massive magical war between the ancient elven nations that left one of the moons shattered and split the world between the skyworld, the overworld, and the underworld. The second came after elven civilization recovered enough to start experimenting with nether magic and demon summoning, at which point demons overran the world, nearly driving magic-using life to extinction and forcing the elves to seek refuge in the underworld, where they became the drow.
The Ends is set in a post-nuclear wasteland, but that's only the beginning of the wierdness. Apparently the nuclear apocalypse set up a "Groundhog Day" Loop, forcing its inhabitants to endure an endless cycle of death and rebirth.
FreakAngels is heavy with this. "London is drowning," seems to be the catchphrase here. Significant portions of Great Britain (and perhaps the world) are submerged underwater, and it turns out that the eponymous protagonists are to blame.
Planet designated 76432-69-GM in Galaxion had a nuclear war first, then an Alien Invasion (though characters speculate that the aliens may have in fact caused the war, but there's nothing solid on that).
Implied in Kit and Kay Boodle, of all things. The world is populated with furries and has crossovers with a few other comics, at least one of which casts humanity as the bygone predecessors of furkind, and humans themselves only appear in classical artwork.
Magical Misfits is set in the far future after magic returned & killed some humans while changing others into creatures of mythology.
Neo Kosmos concerns human kids being raised in captivity by aliens after Earth's destruction, with an archived copy of Wikipedia as their only connection to their ancestral planet.
In Not A Villain, some unknown disaster has completely decimated the world. The survivors live in the ruined cities, some of them trapped with no way out.
O31 is set in San Francisco in a world where all electricity has simply and mysteriously disappeared (which was followed promptly by gigantic explosions worldwide).
Off-White takes place after a 300+ year winter destroyed much of human civilization.
Only Human takes place 500 years after the end, with humanity as we know it gone.
The Order of the Stick is set on what turns out to be the second universe, after the first was destroyed by an Eldritch Abomination called the Snarl. All may not be as it appears, however, as it was recently revealed that the first universe may still exist.
Paonia Pawns visits various alternate worlds suffering through versions of this.
Post Nuke takes place following a nuclear war that played out eerily similar to the biblical apocalypse. A mad dictator took over, nuclear fallout poisoned a third of all water and a third of all land, and there was very little warning of the first shots in the Last War being fired-people say it came like a thief in the night.
There are also a couple alternate universes where, while the most of humanity hasn't died, they have been transported into other dimensions, leaving very few people behind. In one there's no one around but an Alternate Universe Riff and six billion butterflies that replaced every single person on Earth.
Soul To Call: Referred to as 'the Fall'. Two thirds of the human popular were wiped out, and malicious supernatural forces seem to have filled the void they've left…
The prologue of Stand Still, Stay Silent showed the first few days after the discovery of a mysterious "rash illness" through the eyes of a several groups of Scandinavians who either got stuck in isolated areas or ran for the hills as the disease spread. The story itself picks up 90 years later with their descendants. Exactly what happened, and whether or not the character's beliefs that Trolls and Giants rule the world outside of Iceland and the few tiny enclaves they live in are true, is still unclear.
UNA Frontiers. Notable for taking place three hundred years later, and for the conspicuous lack of biker gangs.
Unicorn Jelly takes place in a strange pocket universe where the laws of physics are different from ours. Some time in the past one of the triangular "worldplates" where humans and natives lived was destroyed by something resembling an atomic bomb, resulting in a rain of debris that destroyed other worldplates, creating a chain reaction of destruction that will eventually obliterate every worldplate in this finite but unbounded cosmos. It's later discovered that new worldplates will gradually coalesce out of the debris.