If you can find the old X-men graphic novel God Loves, Man Kills, you should definitly grab it. To me, that marks the point when they started really portrating Magneto in a sympathetic light (though there had been hints of that before). Faced with the genocidal hatred of anti-mutant preacher Stryker, Magneto's cause made a lot more sense. Good story, good art, though I can't remember the artist.
Of course, Marvel seems to have turned Magneto into a straight-up villain again, but for awhile he was an excellent anti-hero in Marvelworld.