The X-Men: M-Day never happened. Cable didn't die approximately six times in the last few years, meaning he was still allowed to be active in Cable & Deadpool, which is still published. Bishop never went rogue. Xorn never happened. All these "Young X-Men" characters are occasional guest characters at best. Beast doesn't look like something out of a Cocteau film. Chamber is in no way related to Apocalypse, because that's possibly more retarded than W. Earl Brown in There's Something About Mary
. Oh, and Gambit's dead or something. No one's really bothered to check up on him because everyone could care less.
The Hulk and World War Hulk: Rulk never happened. Devil Hulk rears his ugly head every so often. Abomination is alive. Rick Jones is in critical condition following WWH. The Falcon kicks Mister Gideon's ass and disowns him as a blood relative. Bruce Banner has absolutely no children at all, on this or any other planet.
Moon Knight: Everything after #13 of the current series is a hallucination.
Captain Britain and MI:13: Pete Wisdom most certainly did not hang an obnoxious lantern during Secret Invasion. Whatever really happened was so awesome it could not be conveyed without destroying our minds, so "No more Skrulls" was how most human brains processed it.
Spawn: Todd McFarlane really did have a plan. And it was awesome.
Ultimate Marvel: Mysteriously ceased publication after the last issue of Ultimates 2.
52/Infinite Crisis/DC Clusterfuck: The Question, not Blue Beetle, died investigating Maxwell Lord's illegal activities, which most certainly had nothing to do with Infinite or Final Crisis, as those never happened. Blue Beetle, not The Question, died of cancer while training his replacement (Jaime Reyes, not Renee Montoya). Much more fitting deaths, as The Question was a detective and BB was already a legacy hero. John Henry Irons never stopped being Steel. Barry Allen is dead. Jade, Bart Allen and J'onn J'onzz are alive. Kon-El tripped on his shoelace and broke his neck on a giant piece of Kryptonite. Grant Morrison's Batman run? Never heard of it. Also have never heard of Geoff Johns at all, I've decided. And what's a Hawkman?
Fantastic Four: Franklin and Valeria's ages are more consistent and don't make me feel like Peter Parker and Bobby Drake should be fifty.
More Superman: Kal-El and MAYBE Zod are the only survivors of Krypton. If and when Zod comes to Earth, he is able to turn public opinion against Superman in a way that Luthor could only dream of by using his brilliant military mind -- and gaining an army of human followers. Becuase that's scarier and so much more awesome than having a few hundred thousand Kryptonians or whatever on Earth. And I would accept an amalgamation of comic book and Smallville continuity in regards to the Luthor family dynamic as backstory.
Thor: Every single time he sees Iron Man, he find an excuse to spit on his armor at least once.
Secret Invasion: Jarvis was replaced only shortly before the story began, so that Aunt May was having standard human sex instead of the intergalactic kind.