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.
Age of Apocalypse
Earth-295, first iteration.This was an alternate timeline resulting from Xavier being killed by his son, Legion, in the past.
Days of Future Past
Earth-811.An alternate future timeline in which mutants have been hunted nearly to extinction.
Earth-807128.This is a future, "what if," type scenario in which Hulk rules most of America and Wolverine and Hawkeye (now both old men) take down the bad guys responsible for the corruption of the country.
House of M
Earth-58162.A timeline in which mutants are the ruling class, and Magneto is their leader.