I've griped about how I think Dr. Who and BBC Sherlock failed when it came time to depict their protagonists' nemesis. In the case of Dr. Who, it is another Time Lord called "The Master," and in Sherlock Holmes's case it is Professor Moriarty. Every Batman needs his Joker and every Superman needs his Lex Luthor.
Thinking through your antagonist is as important as your protagonist and his/her love interest.
My complaint with BBC Sherlock is that Professor Moriarty seemed exactly like The Master who seemed like a nasty schoolboy. True, nasty schoolboys personify evil, but they needn't be taken that seriously. (Unless putting one over your knee and spanking him is not an option.) I guess that's my complaint: If the villain is just like someone you've spanked, s/he falls short of being taken seriously.
Likewise, fellas with monocles and long-haired cats don't work for me. But instead of enumerating what's wrong with other villains, I'd like to say what I think is right with one. I seek a Specification for Antagonist Design.
In World War II, the Japanese Zero was a superior aircraft in several key aspects. Nevertheless, the Americans learned how to avoid its strengths and exploit its weaknesses. Avoid a turning fight against a Zero, and if you can't, get outta Dodge. That's how conflicts work in real life and that's how your stories should work.
Stories without conflict suck. And where conflict is concerned, it takes two to Tango. Thus you want to think carefully about your protagonist's dance partner(s). The best villains have several admirable qualities about them. Sure, Gabbar Singh is evil, but he's got a sense of humor and irony and he loves to laugh--before he shoots them. Darth Vader was a sensitive soul easily disturbed by his co-workers' lack of faith--before he choked the life out of them. The Operative was motivated by his faith.
Greek/Persian conflicts of antiquity. We relate to the independent-minded Greek hoplites who are vastly outnumbered by a host of Persian slaves, but win because they are free men who can seize the initiative on the battlefield while their opponents await the commands of their masters. Thus your story will resonate better with Western audiences if you have a feisty band of Rebels outmaneuvering the giant Empire.
The circumstances needn't be martial. You can write the same conflict between Preston Tucker versus the Big Three automakers with the same asymmetry.
Because companies are generally larger than readers, it's common to make some Corporate Type the villain. Given the amorality of common corporate governance, this is not a stretch. But Big Labor and Big Government work just as well in the role of Persians waging a war of attrition. And since the only good politicians in Washington are Whigs (and long dead) you can show bipartisan villainy. If you want to make Big Religion the villain, choose one that is not in the habit of chopping people's heads off.
That's where I'm at right now. I'm putting together a villain who's motivation is money. He won't blow up the world, because that would destroy all the shops where he spends money. He won't kill everyone, because then there would be no one left to be minions. He doesn't feed his minions to sharks, because it reduces minion-morale. However, his minions are well paid, they have full health insurance with dental, and a generous 401k matching plan.
In other words, he's exactly like me, but with a few billion dollars.
Well, he's different from me in one regard: I'd waste time in the third act gloating about the details of how my nefarious plan works. This villain would just kill the hero and move on to the next item on his Things To Do Today list.
Solzhenitsyn said the line between good and evil runs through the heart of every man. This means you should show the stuff on the good side of the line in the villain's character. Once upon a time, that might have meant being a pious, church-going man, but the Hollywood stupid tax has made religion a telltale of villainy. In choosing the good you put into a villain, you risk making him more sympathetic than your hero.
So, what good attributes do you think should inhere within the character of a villain?