Give your antagonist a backstory. People aren't born bad. There are lots of reasons why someone turns out bad. Sometimes it's a chemical imbalance in the brain. Sometimes a person's upbringing leads them down a dark path. It doesn't matter what reason you give for your antagonist's bad behavior as long as he isn't evil for the sole purpose of giving your protagonist someone to go up against.
Make your antagonist empathetic. We don't have to like him, but we should at least be able to understand why he does what he does. We should be able to see through the eyes of your antagonist and understand the story from his perspective as well as from the perspective of the protagonist.
Keep in mind that not everything is black and white. There are shades of gray. Not every antagonist is all bad; not every protagonist is all good. Exploit this concept when you develop your characters. Give your antagonist a few good traits to go along with the bad. Show your antagonist in a moment of weakness.
Make your protagonist worthy. Do not allow your protagonist to get the best of your bad guy all the time. Don't devalue your antagonist because you're busy making your hero look good. Sometimes the bad guy wins.
Read as much as you can. Watch as many movies as you can. Study antagonistic characters created by other writers. Ask yourself what makes them work? Hannibal Lecter is a good example of an antagonist that works. He has a likable personality. He's bad, but there are villains in those stories that make Hannibal look good. Magneto from the X-Men is a good example of shades of gray and evil being relative. From Magneto's point of view, he's a good guy.