He played Dr. Moon in two episodes of Doctor Who ("Silence in the Library" and "Forest of the Dead"), and I was really taken with him. I also remember his intensity in Alien vs. Predator and the James Bond movies he was in (Die Another Day, The World Is Not Enough and Tomorrow Never Dies). He's got an impressive acting resume, and I think he would have made a wonderful Doctor (and I know he was named as a possible candidate at one point).
Lots of good suggestions (I particularly enjoyed the thought of James Marsters in the role, or Ewan McGregor, or Simon Pegg). I hope Matt Smith is up to the challenge!