1. Think differently than your characters. Superman is good because of his morals. Lex Luthor is evil because of his. Take one or two aspects of your characters and skew it. Twist their ideas and warp them into a new, if not alien, set of morals. Make the players question their's.
2. Think BAD-ASS! Want to draw attention to your villains' villainy? Give them shinier toys. Give them bigger cars. Give them the girls/boys. Give them bigger hair. Make them transform into cooler things. Villains always get cooler clothes! Except for Batman and Gambit.
3. Think "street cred". Nobody wants to hear a giant backstory for an NPC. Don't waste your time with it. Let the villains' actions speak for themselves. Kill innocent villagers. Smash two planets together "just to see what happens". Push limits. Push buttons. But still give them a motivation. A driving force behind his/her actions. Players should have every reason to fear the moment they actually meet the head villain(s), let alone fight them.
To really go the extra mile, strive to have a villain who can blur the lines of morality. Some good examples are Alonzo Harris in the film Training Day, played by Denzel Washington, and Ozymandius from the Watchmen comics and trade paperback. Both are good uses of your time.