Magneto- New X-Men: Planet X
In New X-Men Vol. 6 #146- #150 "Planet X", a villain named Xorn uses his abilities to make a "special class" mutant named Dust attack Charles Xavier. As the attack begins, Xorn imprisons Dust in a jar (sort of the way Spider-Man vacuums up SandMan in Amazing Spider-Man #4) to keep her from interfering; and Xorn removes his helmet to reveal that he is actually Magneto in disguise.
At this point in the story, Xavier has been regaining full functionality/mobility of his body due to the "nanite sentinels" implanted in his body by Cassandra Nova. Magneto, after his identity reveal, explains that he is the one responsible for the sentinel implants and, in that way, he is responsible for Xavier's improvement. Magneto uses his powers to undo the work of the nanite sentinels and cripple Xavier once again- trapping him in a glass tank from which Charles Xavier cannot escape.
Magneto's ultimate goal is to reverse Earth's magnetic field to create "Planet X", a world where mutants have the advantage and rule over human kind. Magneto and his followers begin transforming Earth by laying waste to New York City. The mutants round up human inhabitants of New York and force them into concentration camps to await extermination in "crematoriums". Magneto and his band of mutants murder over 5,000 humans in crematoriums before the end of the book.
Planet X is an important offering to this list because it shows that Magneto is willing to become the very thing that he hates in order to fulfill his own purposes. Where, in the beginning, Magneto was scared of a human holocaust against mutants- he is now comfortable enough in his evil to enact a holocaust against humans.