I love Tom Baker. So much.
Both Tennant and Matt Smith give him a run for his money, though.
I have a lot of fondness for Hartnell, Troughton, Davison and Eccleston. Especially Troughton, but their order in a list will always vary with my mood or time of day.
Pertwee is a special case, because there's a lot of gold in those seasons, but Pertwee himself never feels properly like "The Doctor" to me. He feels like a character from a 60s spy show. I don't know why aging spy doesn't work for me, when grumpy grandfather, hobo, bohemian and ivy league student all equally do, but somehow it won't click.
McCoy, McGann and Colin Baker are hard to quantify because of the often atrocious writing. McCoy feels like he could've been one of the greats, but he never got to shine.