Lauren Donner, producer for the first two movies, has said the movie studio is interested in producing two spin-off films. One film will star Wolverine, in which Hugh Jackman will reprise his role as the clawed warrior. Screenwriter Sheldon Turner is currently working on bringing Magneto to the big screen in his own spin-off film.
The plot will deal with the character's friendship turned sour with Charles Xavier. Turner has stated that "It's going to take place from 1939 Auschwitz up to 1955 or so." Although it at first appears unlikely that Ian McKellen will reprise his role, recently he stated that he would actually be playing a younger incarnation of his character due to a CGI effect which is able to make him appear younger. Rebecca Romijn, who plays Mystique in the X-Men franchise, has been approached about a Mystique film.
Reputable movie news site http://www.superherohype.com is now reporting that X-Men: The Last Stand screenwriter Zak Penn is now writing a third X-Men spin-off film as well.

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I forgot to add this spoiler from X-Men III: The Last Stand and wasn't bothered to edit my post. If you didn't stay after the movie finished and watched the credits give this a read...

(Highlight to read)
Good ol' Charles Xavier is still alive. If you remember that guy that was in the hospital in that video near the start of the movie that had no brain function, well Xavier transferred his own consciousness into that guy just before he died by the mind of Phoniox.