I have quite a few on top of my head! And probably more anyways...
Shogo Makishima from Psycho-Pass, while he was ultimately just some pitiful milk boy that cried for attention he is very literate and artistic. Also in one scene he actually kicks ass and, being one of the older good works from Urobutcher, kills one of the main girls friends in front of her.
Count Saazbaum from Aldnoah.Zero, as terrible as the entire show was, he was a character I really fucking hated at the start but really loved in the end! I can't really explain why, it simply happened... .
Dr. Ver from Symphogear, while the anime got worse and worse, he was cool enough of a dude to be recycled for no other sake but fangasm hype. Also he is probably the only one who sees himself as a hero rather than a baddie. He basically goes around wanting to be recognized (oh what a surprise) and be noted down in history for all eternity, he got a mad-scientist laugh going for himself too. He isn't really outstanding but I still enjoyed him.
Maou from G-Senjou no Maou, I might be a bit biased because that was my first VN I read and that's ages ago, but he is simply, well, a bad guy and the way how he gets shit done is simply a good read. He is just... really solid.
Saya from Saya no Uta, because our Cthulu-loli-deity that plans to turn the entire planet into some hellspawn deserves a spot.
Majorita from Disgaea 5, now, Story-wise, that game is a pile of
tropes crap, but I really, really hated her and even after she, as mandatory in every other Disgaea, joined me in the postgame I continue to despise that bitch. Idc if you got some sob sob sad childhood, I fucking hate you. Basically she wants a 'Utopia' and helps the antagonist out who promises her said Utopia, she is kind of a necromancer and kills as she pleases while enjoying to torture other people.
Luca Blight from Suikoden II, I only started that game a while ago and while he isn't even the end-boss (but kinda main antagonist) he just reks. He is an asshole, evil and
just a human and you take shitload of effort to actually take this guy down.
Asakim Dowin from Super Robot Wars. Now, he, or should I say it? is just another being with a super edgy background. In one of the games he pretty much mind-breaks a heroine. He basically kills her friends in front of her, rape is implied too! And later on through alternate dimension shenanigans he manages that said heroine meets with the murdered characters and they are actually hostile against her. I also like his mech and theme :3
Also since
@Hellis mentioned Nox, Qilby deserves a honorable mention too! Funnily enough I'm going to attend the German Krosmaster Championship next week :P
EDIT:
How could I forget Melvin from Yugioh abridged?! Easily best villain ever.