Hidden Names
When Mystique is looking at the computer, when she pulls up Stryker's file, there is a file named "Remy Lebeau". Remy Lebuau is Gambit's real name.
During the newscast talking about the attack on the president, the news anchor is talking to a scientist, his name is "Hank McCoy". Hank McCoy is Beast's real name.
Other File Folders: "Franklin Richards" and "Muir Island". Franklin Richards is the (mutant) son of Reed and Sue Richards (Mr. Fantastic and the Invisible Woman of the Fantastic Four). Muir Island is the site of Moira MacTaggart's mutant genetics research lab.
Character from X3?
At the end of the movie, right before the credits, during Jean Grey's soliliquoy, if you look at the water, you can see a faint, orange outline of the Dark Phoenix (another character from the X-Men comics).
