20th Century Boys by Naoki Urasawa; the second half of the story is set in Japan after a former cult leader known only as "Friend" controls the entire world.
"The Age of Apocalypse" is an alternate reality of the X-Men. Attempting to kill the mutant Magneto in the past, before he can become a threat, the time-traveler Legion instead killed his own father, Charles Xavier, who took the shot to save his friend of that time. In this timeline, Magneto took the dream of Xavier for himself and started the X-Men, while the mutant Apocalypse created a dystopia where humans were destroyed. This dystopia would be erased from existence by a second time travel by Bishop, who prevented Legion from killing either Xavier or Magneto and so restored the usual Marvel continuity.
Akira, also set in a post-nuclear Tokyo, touches on themes like youth alienation and government corruption.
Alpha Girl, a comic about a group of survivors trying to survive a zombie apocalypse while working to save the brother of one of the group
American Flagg is a comic book series created by writer-artist Howard Chaykin, published by First Comics from 1983 to 1989. A science fiction series and political satire, it was set in the US, particularly Chicago, Illinois, in the early 2030s.
Appleseed by Masamune Shirow is a science fiction manga which combines elements of the cyberpunk and mecha genres with a heavy dosage of politics, philosophy, and sociology.
Attack on Titan by Hajime Isayama follows a group of humans as they try to survive and prevent mankind's extinction from the terror of the Titans.
"Days of Future Past" is a dystopian future of the X-Men, in which the Sentinels, robots entrusted with protecting the human race from the mutants, take control of all human society. This dystopia is erased by time-traveler Kitty Pryde, who goes back to the present and prevents the events that would lead to the dystopia.
Eden: It's an Endless World by Hiroki Endo is set in a near-future world where a biological agent has wiped out approximately 15% of the world's population, while leaving a much larger number crippled and traumatized. Political and religious upheaval drastically change the balance of power between nations and organized crime, with the two sometimes becoming indistinguishable.
Ruins by Warren Ellis is the Marvel Universe in which the myriad experiments and accidents which led to the creation of superheroes in the mainstream world instead resulted in more realistic consequences: horrible deformities and painful deaths.
Transmetropolitan by Warren Ellis concerns a partially dystopian, postcyberpunk take on our world, some unspecified time from now. Nearly everyone lives in "The City," which is overrun with pollution and chaos.
Watchmen by Alan Moore depicts an alternate reality where masked heroes actually exist in American society, and how that affects the history of the twentieth century. The book is marked by a strong sense of alienation in a hostile society.
Y: The Last Man - almost all male mammals in the world have died except for lead character Yorick and his male monkey Ampersand.