Tom Baker is still my favorite incarnation of Doctor who, although I quite liked the Christopher Eccleston and David Tennant versions as well. I'm not sure what it is about the latest Doctor, Matt Smith, but he just misses the mark for me. I recently watched the newest Christmas Special, and by the end I was hoping for another regeneration, but it looks like Smith will be staying in the role a bit longer. It's not a deal breaker for me, because the show is still filled with a ton of imagination and Dr. Who has one of the best rogues galleries outside of comics.
Has the Spectre appeared in the New 52 yet? I don't think I have heard anything yet, but I am sure that it is only a matter of time. When he does show up, it will be interesting to see what his appearance will look like and who his host will be. Let's hope he will be goatee-free this time around.