I want to watch/read more content that features evil protagonist. Please do not recommend shows/manga that have protags who are "fake evil". Manipulative and scheming is a plus.

Already watched One Outs, Code Geass (not evil but added because I do not want anyone to recommend this to me), Youjo Senki, and Akagi a long time ago too.

Aku no Kyouten comes immediately to mind.
Anne Freaks sort of, though I don't think it's executed particularly well here.
Funouhan maybe.
Kami no Kodomo
Kami-sama, Ki-sama o Koroshitai. sort of.
Litchi Hikari Club
Violence Action sort of (she's not exactly "evil", just a sociopath)
Wolfsmund

If you're fine with schlocky gore-survival games, then later followups to Jinrou Game devolve into this. (Particularly Beast Side and Crazy Fox, both of which feature protagonists hell bent on ensuring that they live and everyone else dies.)