This is revealed on the bonus disc of the DVD. Ronnie Drake (Iceman's brother) is the one who alerts the police of the fact that there are mutants in his house when Wolverine, Rogue and Pyro are there with Bobby. On the DVD, there is a section called 'Galleries' which has a shot of Ronnie's bedroom. On his wall, there is a big poster with 'Mutants Suck.' written on it, and another which says 'Is he one of them?'
The entire computer list that Mystique is looking at on Stryker's computer are mutants from the Marvel universe: Guthrie (2) are brother and sister Sam and Paige, Cannonball and Husk, Keniucho Harada is The Silver Samurai; Garrison Kane is Kane from the Weapon X program; Remy LeBeau is Gambit; Eric Lansherr is Magneto, though it is supposed to be spelt Erik Lehnsherr; Artie Maddicks is Big Eyes; Jamie Madrox is Multiple Man; Xi'an Coy Mahn is Karma; Maximoff (2) are the brother and sister Pietro and Wanda, Quicksilver and Scarlet Witch of the Avengers, both are the children of Magneto; Kevin McTaggart is Proteus, Son of Moira McTaggart; Danielle Moonstar is Mirage, Psyche; Ororo Munroe is obviously Storm; Franklin Richards (You only see the "Lin Richards" ), the son of Reed Richards (Mr Fantastic) and the Invisible Woman (Sue Richards).
One of the security guards listed in Stryker's files was Tom DeSanto, the executive producer.
When we see Magneto for the first time in his plastic prison, the music that is playing in the background is the same classical piece that plays in Hannibal Lecter's cell in The Silence of the Lambs.
When Stryker enters the code to enter Cerebro 2, listen carefully - it's the 5 note sequence from Close Encounters of the Third Kind.
Many of the attack moves that Wolverine does during the film, especially during the mansion invasion, are the exact same special finishing maneuvers used in the video game 'X2: Wolverine's Revenge' which was released shortly after the film.
Magneto's line 'When will these people learn to fly?' is a reference to the fact that Rogue and Storm can both fly in the comics.