X-Man/YMMV

Complete Monster: Post-retool issues introduced a number of them. The Gauntlet, a group of mutants who stole the children of the species with an extremely low birth rate and harvested them for organs effectively commiting a genocide. An alternate universe version of Jean Grey who made Nate destroy Quito killing thousands, murdered a little kid, Mind Raped and killed an unknown number of her genetic sons (after having sex with them) and tried to destroy half of the world. Qabiri who destroys entire worlds. From the earlier period we have Holocaust who very definitely established himself as such in his home reality.
Ensemble Darkhorse: The series itself for Age of Apocalypse crossover.
God Mode Sue: Nate has been compared in power to the Phoenix Force, practically unbeatable even by the standards of the X-Men universe. When fanficcers get their hands on him, it gets worse.
Jerkass Woobie: Threnody.