I dont have an all time favourite, but these are some of my faves from each series:
Series 1: The End of the world (nice variety of characters) Dalek (first apperance of a dalek) The parting of the ways (a regeneration is always nice (sometimes))
Series 2: New Earth (good story) School Renunion (Sarah Jane and K-9 return: what more is there to say?) Rise of the cybermen/Age of steel (love the cybermen) Army of Ghosts/Doomsday (Daleks vs Cybermen...........bring it on)
series 3: okay, i do have a faourite this series. Utopia, i love The Master's regeneration, and I love The Master
series 4: The End of time parts 1 and 2 (excellent story, simply brilliant)
series 5: Victory of the daleks (Dont like the new daleks, but i do like the episode) The Beast Below (good episode, i wanna see the smilers return) The Pandorica Opens/The Big Bang (Brilliant way to end the series)
classic: i havent seen many classic episodes, but out of the ones i have seen is The Deadly Assassin. The Master is my favourite doctor who villain, and i like all his episodes but The Deadly Assassin/The End of time/Utopia are my favourites
"You're born alone and you die alone and this world just drops a bunch of rules on top of you to make you forget those facts."