1. Magneto: Professor Xavier’s best friend-turned-arch nemesis is the quintessential arch villain. Magneto is always a threat, no matter where he is on Earth or in the universe. You can count on him to oppose the X-Men on general principle, even when he has to team up with them. And yet, there are arcs where he is the leader of the mutants, and others where he and Charles combine to become the malevolent near-omnipotent Onslaught.
2. Mr. Sinister: Sinister wreaks havoc solely because he’s obsessed with the Summers-Grey bloodline. He’s a weirdo, but he’s powerful and generally involved when he is least needed. His involvement has led to the creation of Cable, the Legacy Virus, and the death of Madelyne Pryor among other things. Never underestimate the power of weird when Mr. Sinister is involved.
3. Cassandra Nova: A mummudrai who is the twin sister of Charles Xavier, Cassandra Nova is behind a lot of the foolishness seen in later X-Men arcs where Xavier dies. She has a hatred of Charles because he won their battle in the womb. She’s gained sentience and a body and generally means to wipe out humanity at large, starting with the massacre of mutants on Genosha.
4. Stryfe: The time-traveling terrorist clone of Cable is terrifying for several reasons, starting with the Legacy Virus. In X-ecutioner’s Song, Stryfe created the Legacy Virus which started out affecting only mutants and then moved on to regular humans, too. The fact that he looks like Cable and that no one can tell them apart is a problem. Having the same processes as the Omega-level mutant is an even bigger problem.
5. Apocalypse: No list featuring X-Men baddies would be complete without mention of the greatest and first mutant, En Sabah Nur. Apocalypse has destroyed entire realities and been one of the most, if not the most, oppressive threats the X-Men has ever faced. Apocalypse’s intellect and capacity for creation and destruction is beyond comprehension, and he is the gold standard for most X-Men villains to look up to.