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Depends if you count the Master/Davros, depends if you count just TV and depends if you count appearance or villainous intent... If you count the Master, then it's him. If not, it's Davros. If you don't count either, it'll depend on if you count audios and novels or not. Sontarans are the next highest recurring villain, but then you'd have to ask what constitutes as an 'evil alien specie appearance' as Strax the Sontaran has appeared in so many episodes that it would elevate the Sontarans to third, but he's hardly a villain, so it depends if you count that or not.
As for favourite Doctor, it's unquestionably Tom Baker's 4th incarnation, followed by Jon Pertwee and Patrick Troughton. The period between 1966 and 1981 was unquestionably a real golden era for the show and was the peak of it's popularity.
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