I've got to say that series 5 (with the mystery of the crack) was, by far, the best series arc we've had so far.The overreaching plot point was introduced in the first episode, tension built as more information about the crack was learned, and the conclusion was satisfying, made sense, and still left room to continue the story on.
source: Hispter Doctor
So what about you? What is your favorite series arc?
Tomorrow: Your favorite music/song from Doctor Who.