Marvel, and comics in general, have always had a tricky time juggling multiple continuities. DC has their Infinite Crisis resets and Marvel has the Omniverse. With Marvel, there are hundreds of different universes and realities. The concept that every decision you make spawns a new universe is prevalent in the Marvel Universe. But which of these realities, universes, and timelines are the best to come out of Marvel?
All of the "What Ifs" spawn new alternate realities, universes, and earths. So, say the Venom Symbiote had overtaken Spider-Man. That would be its own universe, in which every character existed, dealing with the ramifications of that change.
For example, the standard Marvel Universe, the classic iteration, started in the 60s, is Marvel Earth-616. The ultimate universe with ALL of the characters rebooted and reimagined to modern day is Earth-1610. Meanwhile, the film universe with variations on all characters for films is Earth-199999.
It can be confusing, and it's certainly complicated and impossible to keep all these realities straight, but it does help keep continuity a little bit more on the right track. These are the best alternate universes and timelines in Marvel Comics.
http://www.ranker.com/list/best-alternate-universes-and-timelines-in-marvel-comics/ranker-comics,
2099: World of Tomorrow
Earth-928
This alternate took place in the 90s, to be 100 years ahead and to meet our future heroes... and we're still catching up.
Earth X
Earth-9997.
A Marvel title inspired by the artwork of Alex Ross.
Days of Future Past
Earth-811.
An alternate future timeline in which mutants have been hunted nearly to extinction.
MCU (Marvel Cinematic Universe)
Earth-199999.
Beginning with Iron Man (2008) this universe includes all Marvel Studios film continuity, and all film and TV tying into The Avengers. Spider-Man, X-Men, Fantastic Four, and other studio films do NOT fall under this universe.
Marvel Animated
Earth-92131.
Continuity for all 1990s cartoon iterations of the Marvel characters including the "X-Men" and "Spider-Man" animated series, and their print counterparts.
Age of Apocalypse
Earth-295, first iteration.
This was an alternate timeline resulting from Xavier being killed by his son, Legion, in the past.
Ultimate Universe
Earth-1610.
A remaining and modernization of the entire Marvel U for the new millennium. It began with best selling Ultimate Spider-Man title.
Amalgam
Earth-9602.
A crossover event years in the making! After the DC vs. Marvel mini-series, the two industry titans blended their universes creating an amalgamated universe of heroes.
Larval Universe
Earth-8311.
This was the parody universe - home of Peter Porker the Spectacular Spider-Ham, et al.
Galactic Universe
Earth-691.
This timeline was set in the the 31st century. You know, space. Home of the Guardians of the Galaxy.