This is always really tough and could change depending on stories that I've seen recently. Also, many are tied and trying to distinguish between them is pointless. So, I've got several tiers where everyone in a tier is essientially equal. From best to worst:
Tier 1: Smith, Davison, T. Baker
Smith and Baker were both definitely born for the role. They exude a certain alieness, naturally. Davison was my Doctor.
Tier 2: Tennant, Pertwee, Troughton, They are all great. Can't really distinguish between them. Just a smidge behind the top tier.
Tier 3: Eccleston, McGann, Hartnell
I've enjoyed all of these Doctors, but certain characteristics are easier to identify as things that I don't like. For both Eccleston and McGann, part of it could be due to the brevity of the time in the role.
Tier 4: C. Baker and McCoy
Ugh. So many of their stories and just can't stand. Of these two, I think McCoy got the better character while Colin got the better scripts (relatively, though many were bad). But, there are exceptions to that overall pattern. But, generally, not a big fan of either. I've warmed up to Colin a bit over the years, but not enough to get him out of the basement.