1. Yujiro from Baki: Specifically from Baki The Grappler (the first part). The way he was set up was so interesting. I remember reading the moment when he shows his son the severed head of the creature his son had spared just to anger him. His son was angry as obvious, sad, and Yujiro didn't just seem elated but so desperate to make him angry. He was a real interesting villain... then the series kinda made him a meme as it got weirder.
2. Mr. 0/Crocodile from One Piece: While I believe every part of One Piece is better than the last (Though I'm struggling with Elbaph right now; you can really feel it wasn't planned and those first 10 chapters which were pretty much a lego promotion kinda killed the hype too. It's sad to see.), The Baroque Works Saga was like the Lord of the Rings of the series. It took the building blocks of the previous Saga and propelled them to greater heights. Crocodile was an exceptionally manipulative and fascinating villain. And he defeated the protagonist! I thought Luffy was gonna die, and he would've! Thing is though it's early one piece, so he's the evil laugh after dastardly deed kinda villain, the manga was more child oriented back then ignoring all the blood but, he was still written and drawn superbly.
3. Tamaki Damo/Vitamin C from JOJOLION: This is a bizarre one for sure, lol. Tamaki was a truly menacing villain, and unexpectedly so. The fact that this weird rotund guy was dating Hato for a while just to get into the Higashikata Household and torture them for information, and his calm demeanor while doing so. And the way he just about defeated Kira was terrifying. His death was satisfying to say the least.
For once, I can't bring up anything else. The rest of the manga I read have antagonists, not whole villains. I would've thrown Tetsuo from Akira in here, but he was too an Antagonist. I remember feeling devastated when Kei died and he just sorta gave up a bit. He tried so hard to abandon drugs, tried so hard. And yes, I know Wonder of U/Toru is in JOJOLION, but out of spite I didn't include him. I hate Ex-Boyfriend Characters! And I could mention Dio, but to be honest I don't get the hype around him. He's conventional evil, meanwhile Diego is a complex antagonist you can actually sympathize with, sure he's a bad guy, but it makes sense because his mother died of an illness brought on by burnt hands, burned in the first place by a guy she refused to sleep with.
OH WAIT! I DO GOT TWO MORE! We're going out of Manga Territory:
4. Eduardo "Lalo" Salamanca from Better Call Saul: now this guy was terrifying. He seems like a charismatic and funny guy, but all this mask to cover a guy who doesn't even flinch or think about death anymore. And the moment those people around him were killed, he held Jimmy hostage, tried to get Gus killed, TRAVELED TO GERMANY and chopped a guy's foot off! A terrifying force indeed and died with a smile. I still remember the first time he visited Jimmy and Kim at their home, He'd been this mystery up until then but, it all dropped for one of the most nerve-wracking scenes I've watched from a show!
5. Calvin Candie from Django Unchained: Need I explain this one?