William B Davis once said this about his character, "I decided I was the hero, Mulder was the bad guy. Of course as the CSM I was ruthless and unfeeling, but to do what I believed had to be done, how else could I be?." Villains with a worthy cause are always, without fail, the best.
Scorpius and Sikozu.
Scorp needs the wormhole knowledge from John to save the Peacekeepers from the Scarrans. He needs it. If John had cooperated from the beginning, Scorp wouldn't have bothered with Harvy, but he will do whatever he needs to get that information. Sikozu believes in Scorp's cause, but her people come first, and she will do what she had to to protect her race, even if it means betraying her friends.
CGB, Krycek and Marita
CGB is trying to save the world, for himself. It's a good cause, self preservation. Krycek and Marita can only follow him (and each other) to a point, but they were looking towards saving themselves too. When you look at the show flipped over, it's easy to think that maybe CGB was right and Mulder is meddling with things he doesn't understand. Maybe Scully and Mulder should have left well enough alone. (Diana and Spender also fit in here... (But not Knowle Rohrer. Ever.))
Lucius and Narcissa
In Deathly Hallows, their story is very interesting. During Voldemort's first reign of terror, it's clear that the Malfoy's thought that the blood lines should stay pure, but they never seemed to really be as into Voldy. In the end they are trying to help Harry- even though they disapprove of Mudbloods, they understand that Voldemort can not win... cause he's psycho, not political.
Ben and Widmore
One thing I was never fond of on LOST was the way they handled their villains. I get that they were going for the characters being their own villains, but there were not enough complicated love-hate bad guys. That being said, Ben and Widmore were pretty cool. The trouble was that we liked Ben and did not like Widmore, even though they were two sides of the same coin. They both wanted the island, they both wanted to save the world, they both wanted to protect their daughter. I think the idea that Widmore wanted Pen to stay away from Desmond, not because he didn't like him, but because he somehow knew Des would end up on the island, was one of the largest lost opportunities in the last season.
75% of Doctor Who villains.
Preservation of your race, of you and your own. You see it again and again in Doctor Who. In the most recent season alone the aliens in The Lodger, the Saturnynian and the Silurians are all heroes in a way. They are looking out for themselves... and Earth is in the way.
Norrington and Beckett
One thing I like about the Pirates movies is that Norrington is never set up as the villain, he has a job he has to do. Beckett, on the other hand, I've always felt sorry for. His cause is noble, it's for the good of society. Even though we like these particular pirates, when I look at the big picture, I think I'd side with Beckett.
Lex, Tess and Zod
They are all heroes in their own right. Lex and his father are honestly worried about the future of earth with Clark, and rightly so. Sadly, trying to pull a man down from having too much power by making yourself too powerful... doesn't really work. Tess just wanted to save the world and she got caught up in Checkmate, Lex, the Kandorians, the Justice League, all these conflicting loyalties, all these conflicting organizations all with the same goal. Saving the world... from each other. She spread herself to thin and lost their trust. Zod really does want whats best... for his people. What is best for his people... is not best for our people.
In Dunkin Donuts I found a sexy Jeffery Spender look-alike. I stalked him.