I am a big fan of Doctor Who, especially of the Seventh Doctor and his stories. I would say that my favourite Doctor Who story is the 1989 story The Curse of Fenric. Sylvester McCoy is so wonderfully at his darkest in this one. I also love the setting as well. My favourite Doctor's in order are:
Sylvester McCoy
Patrick Troughton
Colin Baker
Tom Baker
Peter Davison
Christopher Eccleston
David Tennant
Paul McGann
William Hartnell
Jon Pertwee
I think the best Patrick Troughton from the ones I have heard and seen is The Tomb of the Cybermen. Even though people say that Tom Baker is the best Doctor, I would say that Patrick Troughton is the best actor out of all the actors that have played Doctor Who.