I can't exactly put them in order(if anything, maybe I should've put them in categories), so I'll just throw them out here and there:
Kyubey. Just fucking Kyubey.
Nobuyaki Sugou(Sword Art Online): WORST. ANTAGONIST. EVER. He had to trap Asuna into ALO to show that he was going to marry her and all that and even had to fucking molest her? Right in front of Kirito? He isn't even a well-written antagonist that can make me love to hate him. I just fucking hate him and was so happy when Kirito destroyed him in the last two episodes of season 1.
Kiryuin Ragyo(Kill La Kill): She had such a horrible desire to invade the world with life fibers and even abused her daughters since their birth to fulfill her plan. Plus, she even molests her daughters, be it to force them to succumb to her or just for no fucking reason. Only redeeming qualities are her rainbow hair and theme music, as well as probably being a good, threatening villain, but that's about it.
Itou Makoto(School Days): Okay, this is honestly one of the worst harem leads I've ever seen in anime. Actually wait. THE worst. How can you be such an douche to all those girls like that and just get bored with them by having sex with other girls? Why the hell were you born?
Saionji Sekai(School Days): I really don't like how she originally tried to push Makoto and Kotonoha together, only for her to butt in like that. I mean, I usually don't mind that type of girl and all, but she really pushes it, especially with her fake pregnancy. Though her slicing off Makoto's head only for her to be killed by Kotonoha was great.
Matou Shinji(Fate/Stay Night): Honestly, what an asshole. I didn't like Sakura all that much, but I already pity her for living under the same roof as this guy. When Rin rejected his offer and slapped him in episode 10 like that, I almost squealed in joy.
Ryuugu Rena(Higurashi): Okay, this girl is crazy as fuck. Yes, I like Yuno, but that's because some complications as well as her backstory were well written and all that. For Rena? She's just crazy as fuck. If Shion(who I also hate a lot) even fears her, then there's something wrong.
Sonozaki Shion(Higurashi): Meakashi-hen. That's all I have to say.
Kasugano Sora(Yosuga no Sora): Her personality is complete shit. She always complains about her lifestyle despite being super lazy and possessive of her onii-chan. Even going to the point of masturbating to him and attempting to commit suicide just because he slapped her. A fucking slap. Yes, I hate incest. But at least Kirino wasn't even about the incest route(but please don't talk to me about season 2's ending, just don't...) Sora, on the other hand, was a shitty character overall.
Tobiichi Origami(Date A Live): I originally thought I would like her. Or at least sympathize with her. But as the series went on with her conflicting ideals, I was almost done with her. Then, the fight she had with Kotori by the end of season 1 led me to hate her a lot. Like, you noticed that you're immoral for murdering Shido, but then you go crazy with destroying Kotori, who was not even the murderer in the first place, leading you to possibly murder dozens of people at that amusement park?
Don't even get me started with her descent from angel to devil spirit in the light novel(yes, I read Volume 10 without watching season 2 for curiosity, deal with it)...
There are also some others I can list as honorary mentions, but I'll only say five to maintain my sanity:
Orimura Ichika(Infinite Stratos)
Shokuhou Misaki(To Aru Kagaku no Railgun)