Ultimate Marvel/WMG

Ultimate Marvel

Thor really was just a delusional Norweigan nurse with stolen technology...
...Until Scarlet Witch altered reality to make Loki, Asgard and Valhalla real. That's why his speech changed from contemporary to pseudo-Elizabethan, and why he suddenly acquired an arsenal of alternate hammers. Wanda probably was responsible for Valkyrie getting powers, too.
 * This is now part of This Troper's personal canon since it's the only way to restore continuity in Ultimates 3.
 * The only other possible reason for the changes is that after Ultimate Power, they went back to a universe almost identical to theirs, but a little... off. Which means the original un-Ultimatum'd UM is still out there somewhere in the multiverse...

The creepy Spider-Man-Who-Is-Not-Spider-Man from Ultimate Avengers...

 * ...is an Eldritch Abomination unrelated to anything we know about.
 * ...is the currently unrevealed Ultimate Enemy of that miniseries and its sequels. Does not conflict with the above.
 * ...is a lost clone.
 * ...is a man/is a woman/is a robot.
 * ...is a Time Lord, and the Ultimate Spider-Car is his TARDIS.
 * ...is Haruhi. Not as implausible as this theory is most of the time.
 * ...is Ultimate Doppelganger, and Mark Millar is on fucking crack.
 * ...is Ultimate Jackal, whose obsession has manifested in "being" Spidey instead of cloning him.
 * ...is Ultimate Bullseye, who is dressed in an off-color Spider-Man suit because he's crazy.
 * ...is Peter Parker from an evil mirror universe, hence the costume difference.
 * ...is something Millar just made the hell up.
 * ...is Ultimate Deadpool.
 * ...is Marvel Zombies Spider-Man. That's why he's kept in an isolation tube.
 * ...will never be seen or heard from again, because a new writer will take over and crap all over continuity again.
 * Official answer? He's a clone of Peter Parker and an alternate Charles Xavier from the future.
 * No, that was just Gregory Stark and Nick Fury screwing with Carol Danvers. We have no idea what the real story is.

Kong wasn't being metaphorical about the Ghostbusters thing in Ultimate Spider Man #15.
Beginning very early on, Bendis dropped hints that the events of the Ultimate universe were all connected and leading to a catastrophic event. All of this will eventually culminate by revealing that the appearance of Mutants and various other superhumans are all portents of Gozer the Gozerian.

The mysterious female shadow behind Quicksilver in Ultimatum: Requiem is...

 * Scarlet Witch-- no, too obvious.
 * This one is confirmed as of Ultimate Comics X issue 5.
 * Ultimate Jocasta, prematurely activated-- whoops, yet another Hank Pym experiment Gone Horribly Wrong.
 * Quicksilver's mother Magda.
 * Valkyrie. Obfuscating Stupidity, anyone?
 * Hela. As a death godess, she loved the whole "killing millions" aspect of the plan, the rest was Quicky's idea.
 * Zarda. Same reason.
 * Dr. Doom in drag! (the one Thing killed was a clone/shapeshifter/LMD/AlternateUniverse Doom/some guy in armor)
 * Nick Fury in drag!

The Ultimate Super-Soldier Serum was derived from studying the Chitauri.
Herr Kleiser had super-strength and a Healing Factor roughly similar to Ultimate Captain America's. What with the UM's tendency to give everything a Meta Origin, it makes sense to tie the last few remaining loose threads together.

Dr Manhatten created the Ultimate Marvel Universe.
The world of Watchmen is dark,gritty and realistic,and the Ultimate Marvel Universe is darker than the normal one.At some point,Dr Manhatten decided to create his own world(similar to the WMG about Superman),however its tone reflected his own gritty and realistic world

Ultimate Wasp knew some Brother-Sister Incest couples
maybe some were some very good friends of hers.

Nick Fury
It was and LMD.
 * Nah, he was just the hulk at the time.

Ultimate Magneto actually had a secret Freudian Excuse.
616!Magneto is sometimes speculated to have some variety of psychic power in addition to the magnetism. Ultimate Magneto had some kind of low-level telepathy or empathy that he never consciously recognized and developed, which left him open to the psychic impressions around him. Considering that the Ultimate Marvel universe is full of jerks, being a psychic sponge at an impressionable age didn't do him one bit of good, and aggravated his preexisting mental instability and supervillainous tendencies.

Having to deal with the cast of The Ultimates in my head would have me tempted to start flipping the magnetic poles.