Among the many easter eggs in the movie referencing other mutants, Singer placed an homage to popular X-man Archangel, who had been scrapped in early drafts of both X-Men and X-Men 2. Notice in the fight scene between Lady Deathstrike and Wolverine...up on the wall there are schematics and prototype sketches of Archangel's metal wings.

In the scene where Mystique is going through the files on Lady Deathstrike's computer to find the guard's profiles, one of the guards is director Bryan Singer (he's listed as "Singer, B").

May be obvious to some people, but I missed it the first time around. Towards the end, when Jean Gray's outside, Nightcrawler says that she's stopping him going out there. When he tries to teleport, you can briefly see the smoke appear round him then disappear as he gets blocked.

In the deleted scene Mystique in Stryker's files from the DVD two-disc special. Mystique read Kurt Wagner's notes. On all the X-rays, we can read "X-ray c13957", and they were all taken in May 22 1984, but they show a full grown man.

The X-Men graphic novel, "God Loves, Man Kills" (some of the plot for the movie X2) the mutant hater's name is William Stryker, the same name as the militant mutant hater in the movie.

What is it with Rogue and seat belts? First she can't get out of Logan's truck in X-men and in this new film, she can't get either restraint buckled and is sucked out of the Blackbird...

Mystique transforms into a blonde woman to seduce the security guard. This blonde woman is actually Rebecca Romijn-Stamos, a.k.a... the very Mystique herself. The only time we see her without the blue makeup...

The ending is very reminiscent of Star Trek II: The Wrath Of Khan. The person with the closest relationship to the leader of the group sacrifices him/herself to save the rest of the group, and just before the closing credits we hear the dead person's voice recite a speech previously spoken at the beginning of a previous film/episode ("Space the final frontier..."/"Mutation..." from the first film). They even left a way for Jean Grey to come back in the next film (apparently in the cartoons she came back from the dead as a phoenix - look at the water and you can see the shadow of a phoenix).

When 'Senator Kelly', William Stryker, and President McKenna are talking in the oval office, they are each wearing an American flag pin.

Two random similarities to "Edward Scissorhands" in this movie. At the start, Nightcrawler looks almost identical to Edward when he's robbing the house - pale, marks on his face, blue baseball cap. Also when Edwards emerges from the house, he's holding his scissors out towards the police, who think they're weapons he's using to threaten them - exactly the same thing happens in this with Wolverine. Deliberate, or just coincidence?

In the comic, Xavier had a son named David Haller who became known as Legion. He was mentally disturbed, suffering from multiple personality disorder. He had several different psychic powers, and each personality controlled a different power. One of them was a young girl. His left eye was green, and his right eye was blue. In the movie, Stryker has a son named Jason. He is mentally disturbed or catatonic. He has psychic powers. In the illusion he creates for Xavier, he appears as a young girl. His left eye is green. His right eye is blue. It would seem that this is supposed to be the movie's version of Legion. Some people also say that Jason is Mastermind aka Jason WyneGarn (or Jason Stryker, I guess in the movie) who has the telepathic ability to create illusion that are completely believable in every way, sight smell, sound.