Dr. Jekyll: God damn you, Hyde! Take all your evil deeds and rot in Hell!
Mr. Hyde: I'll see you there, Jekyll!
~ Conversation between Dr. Henry Jekyll and his alter-ego, Mr. Edward Hyde.

Alter-Ego pertains to an alternate "evil self" held by a normally non-villainous character, or else aspects of a particularly powerful villain or alternate versions of a villain. 

Note: Do not include here Supervillains who have a civilian alter-ego; this category is only for villains who are either an evil persona taken by a normally not evil character (such as Mr. Hyde to Dr. Jekyll), or an alternate form of a pre-existing villain (such as Night-Terror in relation to Nightmare from Soul Calibur). Also, do not add villains who are an alternate reality version of a heroic character. Those are Alternate Reality villains, not Alter-Ego.