Trying to think of my favorite antagonists from all of the books I've ever read is difficult. I know I'm going to leave some awesome antagonists out of the list, but here are a few of my favorites. Warning: most of these contain at least slight spoilers.
Voldmort and the Death Eaters from the Harry Potter series. I couldn't help it. They had to start off this list. I would have listed several different Death Eaters seperately, but I didn't want to clog this list up with Harry Potter characters, so I won't list any Death Eaters individually. I don't think I could ever despise another fictional character as much as I do Voldemort, Bellatrix, and Wormtail (and the next character on this list). They're so well written and so horrible. Plus, I love that we get lots of backstory on Voldemort, and we get to kind of understand why he turned out the way he did.
Umbridge from the Harry Potter series. She's almost worse than the Death Eaters. I can't stand how she does whatever she's told to by whoever has the most power. I swear she would have become a Death Eater early on if she'd known Voldemort was out there and would control the Ministry. Not only does she act like a puppet in order to gain power, she also does horrible things on her own, such as giving a fifteen year old boy a detention where he has to write lines in his own blood.
Coin from The Hunger Games series. I'm putting her on this list but not Snow. Ever since reading Mockingjay I've hated Coin more than Snow. Snow tells Katniss they shouldn't lie to each other in Catching Fire, and he really never does lie. Everyone (except the Capitol citizens of course) know that Snow's corrupt/evil/etc. Snow does horrible things, and sure, he puts on an act when he's in public. Coin, however, goes even farther in my mind. She tries to act like she's on Katniss' side, even to Katniss, and then, she tries to kill her. It's not really that different from what Snow's doing, and yet it seems so much worse in my mind.
Dr. Cable from the Uglies trilogy. She doesn't have that large of a role for most of the books, but the role she does play is very important. She's interesting because she's not really evil. As far as she's concerned, she's doing what she needs to do to protect the society they live in. Plus, she surprises Tally (and me as well) towards the end of Specials. I think that's when I really realized that she isn't that bad of a person. I don't think she thought of what she was doing as wrong, and I can see her justification for her actions. I think she's a very interesting character.
I'd add more to this list, but it's past midnight and I need sleep. Besides, most of the books I read don't have one clear-cut antagonist. I actually realized that in most of the books I read the protagonist themself is also the main antagonist. Still, I hope this list is fun to read, even if it is short. I feel like it's almost unintelligible because I'm half asleep. I'm going to bed before I fall alseep while on the computer.