Magneto- Uncanny X-Men #200
In Uncanny X-Men #200 Magneto is put on trial for his crimes against humanity. Afraid that he will be sentenced to death, Magneto uses the power of his helmet to remove the anti-mutant sentiment from the judge's brain. Tinkering with the judge's brain leads to Magneto being set free and raises ethical questions about whether the manipulation made Magneto's trial more or less fair.
Magneto has been around so long, and has been given so much individual attention, that he is more popular than many of his X-Men adversaries. On a very basic level Magneto's cause is noble, and it causes readers to question whether Magneto is a villain or an anti-hero. When a reader can't decide Magneto's alignment, and they question their own moral compass, that is Magneto's most villainous moment.