As Paul Smith noted, I caught X-Men 3: The Last Stand the other night with him, my wife and daughter, and my good buddy (and fellow comics junkie) Brent. Unlike Paul, however, I'm not going to go into much of the social and political implications (I do think what Paul touched on, however, is pretty much accurate). I usually jump at the chance to do so (I'm working on a guest commentary for Avi Green's Four Color Media Monitor blog), but in this case I'd rather point out the movie's connections to comicbook history.
SPOILER SPACE!! Do not click "continue" if you do not wish to have key details of the movie revealed!!
I had heard good and bad things about the movie since its premiere. I figured I'd like it nonetheless as I'm a big comics fan. (Then again, that's what I said about "Fantastic Four" -- YUCK!) Indeed, I was quite satisfied with "X-3." I had read via various Internet sites that the legendary "Dark Phoenix" saga was a significant subplot to the film, and this is true. Of course, the movie had to make some significant alterations to the Phoenix back-story to make it relevant to the X-Men films. This tends to alienate purist "fan-boys" (which is surely ridiculous, IMO); I think it's terrific that the film's creators wove into the film's history one of the X-Men's comic's greatest stories -- indeed, one of all of Marvel Comics' greatest stories.
The "alteration" is as follows: Jean Grey, who was apparently killed at the end of "X-2," is revealed to be alive, somehow "wrapped in a telekinetic coccoon" at the bottom of the lake. Professor Xavier (Patrick Stewart) reveals that Jean is actually the only "class-5" mutant alive -- the most powerful ever, more powerful than either Magneto or Xavier -- combined! Xavier had to "install" a series of "psychic circuit breakers" in Jean's mind to keep her "dark side" under wraps. This dark side is dubbed the "Phoenix."
In the comic (issue #100 of the "new" X-Men, to be precise), the X-Men had just finished a battle on an earth-orbit space station against the mutant-hunting robot Sentinels (one of which has a "cameo" in the movie -- the X-Men practice fighting against one in their famed "Danger Room"). Jean Grey has to pilot a space shuttle back to earth as only her mental powers can keep out deadly solar radiation from seeping through a hole in the craft. Unfortunately, her power didn't appear to be enough -- but when the shuttle crash-lands in Jamaica Bay (near New York City, of course!), Jean emerges from the drink virtually unscathed, and proclaims herself as the Phoenix.
It's eventually revealed that the Phoenix is sort of a cosmic/psionic entity that "took Jean's place" in her body when Jean was "killed" by the solar radiation. Subsequent retcons of the X-Men backstory have established essentially what is shown in the movie -- Xavier had placed psychic blocks in Jean's mind as a child, and that the Phoenix was always a subconscious part of her mind.
Beginning in issue X-Men #101, Phoenix is in control of her (increased) powers, but when one of the "evil" mutants (named Mastermind) projects illusions into her mind, the "dark" side of the Phoenix force overwhelms Jean and she loses control. She easily bests her teammates (all of whom have been seen in the X movies: Wolverine, Cyclops, Nightcrawler, Storm, Beast) but when she engages Professor X in a telepathic battle, she loses -- only because she was also fighting herself from within. In the movie, Jean utterly destroys the Professor. Also noteworthy is that, during Jean's battle with the X-Men in the comics' pages, Wolverine had an opportunity to kill Jean while her human side had briefly regained control of her body -- but he was unable to do it. In the movie's climax, to save the whole planet, Wolverine barely hesitates to kill Jean.
Monetarily, the movie in no way would have been able to portray what subsequently occurs in the comic. After Professor X defeats Dark Phoenix and re-establishes the psychic blocks in Jean's mind, Jean, the Professor and the X-Men are teleported aboard a starship of the alien Shi'ar race. While Jean first was transformed into Dark Phoenix, she traveled to Shi'ar space and destroyed a sun and all of its planets, one of which was inhabited. As punishment, the Shi'ar want to execute Jean/Phoenix. Professor Xavier manages to convince the Shi'ar empress, Lilandra (who was once Xavier's lover, but that's another story), to allow a battle of super-teams (the X-Men and the Shi'ar Imperial Guard) to decide Jean's/Phoenix's fate. The X-Men lose, but as the victorious Imperial Guard close in on Jean, she once again transforms into Phoenix after seeing her lover, Cyclops, cut down by the Shi'ar super-team. Before the Dark Phoenix is able to take control of her once more, however, Jean manages to kill herself with an alien weapon (the classic X-Men #137).
There was much controversy surrounding the Dark Phoenix story, especially when Marvel decided to "resurrect" Jean/Phoenix. One [preceding] interesting tidbit is that then-X-Men creators Chris Claremont (who had a brief cameo in X-3 as the guy mowing his lawn in the film's beginning) and John Byrne did not want to have Jean killed in the climax issue #137. They were overruled by then-Marvel Editor-in-Chief Jim Shooter, who felt (correctly, in my view) that merely "excising" Jean's power wasn't sufficient punishment for the killing of over four billion people (when Dark Phoenix destroyed that sun, natch).
Claremont apparently never wanted Jean/Phoenix to be resurrected period, and bitterly opposed John Byrne's [later] plot to retcon the whole premise behind Phoenix. From here, things get really hectic and too in-depth with minutiae. One thing I appreciate, though, is that my favorite current comics writer, Kurt Busiek, actually is credited with coming up with the idea of resurrecting Jean that Marvel eventually decide to go with. Ironically, Byrne garnered much of his success by retconning many Marvel (and DC) characters, but this eventually lost its "lustre." Byrne's retconning of the Avengers' android Vision character was widely criticized (and, in another ironic twist of fate, was later ret-retconned by Kurt Busiek in the phenomenal Avengers Forever twelve issue series), as was his "Spider-Man: Chapter One."