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.
Earth-811.An alternate future timeline in which mutants have been hunted nearly to extinction.
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.
Many different earths.An entire long running series spawning HUNDREDS of alternate universes (about one a month), dealing with the concepts of major events going a different way and how it would change Marvel.