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Xanxus of Katekyo Hitman Reborn! is the incredibly badass leader of the Varia, an elite assassination team primarily employed by the most powerful mafia family in the world. He has some amazing full-body scars◊, and he spends most of his time throwing blunt objects at his subordinates and breaking their faces with tables.
Subverted with Zagato of Magic Knight Rayearth . It seems at first that he is the main villain, but then the plot twist happens.
Galbatorix from the Inheritance Cycle is a name you give you child if you want him to grow up to be an evil emperor. It's possible that Galbatorix chose the name, but why is beyond most people; it doesn't roll off the tongue and sounds generically evil. You'd think someone who wanted to take over the world would ease people into it by picking something which sounded nicer. And if Galbatorix is indeed his given name, then he is fully justified in wanting to kick some ass—which raises the question of why he was let into the Dragon Riders.
Pretty much everyone from Sanctaphrax (The Edge Chronicles), but Orbix Xaxis deserves a special mention.
Lampshaded in Unseen Academicals with Dr. Hix, who changed his last name's spelling from Hicks to Hix because a man with a skull ring would have to be mad, or shall we say, even madder, to pass up the chance to have an X in his name.
Xaro Xhoan Daxos from A Song Of Iceand Fire. While he is not really a positive character, he is not actually evil, too. In the series, however, he becomes a main antagonist by the end of the second season.
Jarlaxle, also of Forgotten Realms. He probably won't kill you. He'll just make your life a living hell.
Zaknafein, Drizzt's father, a four-hundred-year-old weapons master who's defeated demons in single combat and can take someone's tongue out with a whip while blindfolded. And depending on the person, enjoys doing it.
All of the Organization XIII members in Kingdom Hearts have names that are anagrams of their human names with an "X" added, like Lea-Axel, Braig-Xigbar, Dilan-Xaldin, etc. Xehanort follows the same pattern - among many other possibilities, his name without the X is an anagram of "no heart".
Xykon, self named for the Xtreme Kool Letterz quotient. Gets (more) homicidal whenever someone spells his name with a Z by mistake - Zs are for pussies. Note the suspicious similarly of the name to the compound Zyklon B, used by the Nazis in death camps. Presuming this was intentional, it provides a good clue to Xykon's general nature.
X. Who's birth name is Elzandra, legal name Alexandra, and happens to be a Child of Prophecy. She also likes explosions. The only reason she wouldn't qualify is her extreme apathy.
Pretty much everybody from the Fire Nation has a Z in their names. Zuko, Zhao, Azula, Ozai, Sozin, Azulon. Worth noting: most the Fire Nationals who don't have a Z in their names were never really antagonists, such as Iroh, Ursa, Piandao, Roku, and Jeong Jeong.