I think your favourite Doctor is the one you watch when you're a certain age. Tom Baker took over when I was about 8 or 9 and stayed in the role into my mid teens, so for me he's the definitive doctor. Jon Pertwee was a tough act to follow though.
Unfortunately after Tom Baker it just kept going down hill until towards the end of Sylvester McCoy's stint. Not counting the very last episode, which looked like a poor excuse to recycle costumes from Cats, I thought the Sylvester McCoy episodes featuring Ace were some of the best since the Tom Baker days. But then just as the series was picking up again it got cancelled.
The revival has done the series proud though. Blink is one of the best Dr Who stories ever, easily up there with older classics like The Green Death, Genesis of the Daleks, Pyramids of Mars, Logopolis...