Parallel universes in modern comics have become particularly rich and complex, in large part due to the continual problem of continuity faced by the major two publishers, Marvel Comics and DC Comics. The two publishers have used the multiverse concept to fix problems arising from integrating characters from other publishers into their own canon, and from having major Serial protagonists having continuous histories lasting, as in the case of Superman, over 70 years. Additionally, both publishers have used new alternative universes to re-imagine their own characters. (See Multiverse (DC Comics) and Multiverse (Marvel Comics))
DC Comics inaugurated its multiverse in the early sixties, with the reintroduction of Golden Age superheroes the Justice Society of America now located on Earth-Two, and devised a "mirror universe" scenario of inverted morality and supervillain domination of Earth-Three shortly afterward, several years before Star Trek devised its own darker alternative universe. There was a lull before DC inaugurated additional alternative universes in the seventies, such as Earth-X, where there was an Axis victory in World War II, Earth-S, home to the Fawcett Comics superheroes of the forties and fifties, such as Captain Marvel, and Earth-Prime, where superheroes only existed in fictional forms.
Therefore, comic books in general are one of the few entertainment mediums where the concept of parallel universes are a major and ongoing theme. DC in particular periodically revisits the idea in major crossover storylines, such as Crisis on Infinite Earths and Infinite Crisis, where Marvel has a series called What If... that's devoted to exploring alternative realities, which sometimes impact the "main" universe's continuity. DC's version of "What If..." is the Elseworlds imprint.
Recently DC Comics series 52 heralded the return of the Multiverse. 52 was a mega-crossover event tied to Infinite Crisis which was the sequel to the 1980s Crisis on Infinite Earths. The aim was to yet again address many of the problems and confusions brought on by the Multiverse in the DCU. Now 52 Earths exist and including some Elseworld tales such as Kingdom Come, DC's imprint WildStorm and an Earth devoted to the Charlton Comics heroes of DC. Countdown and Countdown Presents: The Search for Ray Palmer and the upcoming Tales of the Multiverse stories expand upon this new Multiverse.
Marvel has also had many large crossover events which depicted an alternative universe, many springing from events in the X-Men books, such as Days of Future Past, the seminal Age Of Apocalypse, and 2006's House Of M. In addition the Squadron Supreme is a DC inspired Marvel Universe that has been used several times, often crossing over into the mainstream Universe in the Avengers comic. Exiles is an offshoot of the X-Men franchise that allows characters to hop from one alternative reality to another, leaving the original, main Marvel Universe intact. The Marvel UK line has long had multiverse stories including the Jaspers' Warp storyline of Captain Britain's first series (it was here that the designation Earth-616 was first applied to the mainstream Marvel Universe).
Marvel Comics, as of 2000, launched their most popular parallel universe, the Ultimate Universe. It is a smaller subline to the mainstream titles and features Ultimate Spider-Man, Ultimate X-Men, Ultimate Fantastic Four and the Ultimates (their "Avengers"). The line in many ways both inspired and was inspired by aspects of the new movie franchises in addition to creating younger versions of the modern heroes.
The graphic novel Watchmen is set in an alternative history, in a 1985 where superheroes exist, the Vietnam War was won by the United States, and Richard Nixon is in his fifth term as President of the United States. The Soviet Union and the United States are still locked in an escalating "Cold War" as in our own world, but as the Soviet Union invades Afghanistan in this world and threatens Pakistan, nuclear war may be imminent.
In 1973 Tammy published The Clock and Cluny Jones, where a mysterious grandfather clock hurls bully Cluny Jones into a harsh alternative reality where she becomes the bullied. This story was reprinted in Misty annual 1985 as Grandfather's Clock.
In 1981 Jinty published Worlds Apart. Six girls experience alternative worlds ruled by greed, sports-mania, vanity, crime, intellectualism, and fear. These are in fact their dream worlds becoming real after they are knocked out by a mysterious gas from a chemical tanker that crashed into their school. In 1977 Jinty also published Land of No Tears where a lame girl travels to a future world where people with things wrong with them are cruelly treated, and emotions are banned.
The parallel universe concept has also appeared prominently in the Sonic the Hedgehog comic series from Archie Comics. The first and most oft-recurring case of this is another "mirror universe" where Sonic and his various allies are evil or anti-heroic while the counterpart of the evil Dr. Robotnik is good. Another recurring universe featured in the series is a perpendicular dimension that runs through all others, known as the No Zone. The inhabitants of this universe monitor travel between the others, often stepping in with their Zone Cop police force to punish those who travel without authorization between worlds.
In more recent years, the comic has adapted the alternative dimension from the videogames Sonic Rush and Sonic Rush Adventure, home to Sonic's ally Blaze the Cat. The continuities seen in various other Sonic franchises also exist in the comic, most notably those based on the cartoon series Sonic Underground and Sonic X. For some years, a number of other universes were also featured that parodied various popular franchises, such as Sailor Moon, Godzilla, and various titles from Marvel Comics. Archie has also used this concept as the basis for crossovers between Sonic and other titles that they publish, including Sabrina the Teenage Witch and Mega Man.
The various Transformers comics also feature the parallel universe concept, and feature the various continuities from different branches of the franchise as parallel worlds that occasionally make contact with each other. Quite notably, the annual Botcon fan convention introduced a comic storyline that featured Cliffjumper, an Autobot from the original Transformers series, entering an alternative universe where his fellow Autobots are evil and the Decepticons are good.