Technically speaking, that doesn't exist. By definition, the main character is the protagonist, even if he's evil.
But I know what you mean sooooo, I guess Death Note, Code Geass, Killing Stalking, Aku no Hana, Ayeshah's Secret, Oldman (he's an outlaw wanted for treason, but he's actually a good person, so I guess this is debatable; an amazing read), Tokyo Ghoul, and Watashitachi no Shiawase na Jikan (a must-read).
Any manga where the villain/antagonist is the main character? Thanks! (●'◡'●)ノ