There are a lot of really great villains out there, in books and in TV and movies. There are a few things that make a villain a good antagonist (and they're not always the same, BTW), but I tell newer writers when they ask me that they have to remember a few things about villains.
1) Make the villain sympathetic. At least a little bit. Now that sounds weird, I know, and I'll explain in a minute. We shouldn't like him right away, of course, because we have to grow to love our protagonist and dislike our villain, but at some point we have to understand at least a little bit of why he's doing what he's doing. There are exceptions, and because they ARE exceptions, they can be insanely scary. But if your villain is just a mustache-twirling guy doing something mean for the sole purpose of being mean, well, he'll probably come across as one-dimensional and not very good.
2) One thing you must remember, the most important thing when writing a villain/antagonist:
They think they are right.
They are the hero in their own story. The story you're reading, the story the author wrote, is from the protagonist's POV. But if you were to write it from the antagonist's POV, you'd have to turn it on its head and make that villain the hero. Which is why I usually give my antagonist some kind of backstory, even if it's only in my head, because that will color everything he does. This also can help with the sympathetic bit, if the villain's backstory is kind of sad.
My top-five villains:
1) Maleficent (Sleeping Beauty): She is deliciously bad, but again, she has a reason for doing it. Revenge is a really great motivation for kicking some butt. And she turns into a dragon. Which is just awesome.
2) Voledmort: how can you not love to hate old Voldy? It takes five books to discover his back story, but it's SO GOOD. By the very end, you do feel a little bit bad for him, because he's had a bad life-- orphaned (like Harry), rejected by his birth father who was a Muggle. Who wouldn't be a little bitter against Muggles after that? He wanted to conquer death, and well, things got a little out of control. By the end of the series he's a little more pathetic than frightening, and you still want Harry to win but you still feel a little bad. Voldemort's had a sad kind of life.
3) The Master (Doctor Who): Many people have played The Master over the 50 years the series has been on the air, but the latest reincarnation--oops, I mean regeneration-- was by far the best. I loved to hate that guy! He was bad, evil, mean, and just plain silly. He was a little bit psychotic, but he was driven mad by looking into the Time Vortex when he was a boy. Hey, it happens. And all he wanted was a planet to call his own, since Gallifrey went teets-up. Who doesn't want that? His humor made all the killing and Earth taking-overing just seem a little more fun.
4) The Joker (Heath Ledger version): this is the exception to the rule of the sympathetic villain. You never really know The Joker's backstory, not really. There's no motivation for his behavior that we ever know. And this is why he's so great, so terrifying, because he's one of the very few villains who just wants to watch the world burn.
5) You tell me. Who do you think should fill this spot, and why? What villains do you love to hate?