Tom Baker is my favourite, who had well written scripts that matched his sarcasm, grin and wit. (I grew up watching the B&W Dr WHO series on the ABC, with Patrick Troughton who was good also). John Pertwee who replaced Patrick Troughton was lucky to have some very good episodes written for him, but as a Doctor I thought was a bit feminine for the role.
I never saw enough of the other Doctors to have a least favourite. Perhaps Peter Davison who played the role of Dr WHO like a school teacher.
Check out the average viewer numbers for each of the series - incredible number of viewers and followers for the first 3 series in the 1960s. The popularity peaked with the 4th Doctor (Tom Baker - 1974 to 1980). Apart from the specials, the Tom Baker viewer numbers havent been matched by any of the other Doctor WHO series (and there are far more people living in the UK today and the marketing and promotion is higher).
So I reckon even the numbers back up Tom Baker. The Doctor with the least viewers seems to be Sylvester McCoy, the 7th Doctor (from 1987 - 1989). I think the series was axed in 1989.
http://en.wikipedia.org/wiki/List_of_Doctor_Who_serials