I believe that my favorite character on Stargate Atlantis is Todd the Wraith, because he is a very complicated and interesting character.
Though he is a villain, and always, always has an agenda, he is a very open minded villain with an agenda. He is perfectly willing to work for or against any side, so long as it will benefit his goals, as opposed to a standard villain that is always opposed to the heroes.
He is incredibly good at getting himself put in charge. The first time he is seen on the show, he is dropped off on a planet full of his people, half-starved, wearing rags, with nothing to aide his standing, and in less than a year, he is in charge of a small fleet.
He has a sense of humor, a sense of honor, and great dignity.