I have given this more thought in the last few hours than in all the time the original series was on and I was watching it. I think the difficulty is in separating the Doctor character (and the actor portraying him) from the stories he appeared in.
For example, I always cite Davidson's doctor as the one that killed interest in the show for me, but when I thought about it, it wasn't so much the actor as what he had to work with. Insipid plots, stupid costume, tedious banging on about cricket when there was a lull in the action and surely the least memorable companions.
I never got to see Colin Baker other than once, and I saw that they had just taken the Davidson version and turned the "Stupid" knob up to 11.
I liked McCoy as an actor, but never really wanted to watch his doctor doing what they had him doing with the dreadful selection of people he was dragging in his wake.
I usually cite Hartnell as my favourite, but that is because I remember "An Unearthly Child" and the fact that they had to repeat it the next week before the second episode because so many people wrote in and complained they had missed it, and because William Hartnell looked like my grandfather . The episodes with Hartnell haven't aged well, unfortunately, and his acting was not stellar much of the time, probably due to his illness. I wonder what he could have done with the part if he'd been ten years younger.
Ecclestone stands out for me as light years ahead of the pack. The lone Dalek episode is probably the best Dr Who story I've ever seen (at least until the soppy ending). I'll never forget Ecclestone's terrified "Not possible!"
But I think, against my own expectations, having just watched a Dr Who special on BBC America and done a bit of thinking, Tom Baker takes the cup for me. The plots weren't great much of the time. Some of the companions were asking for a shovel in the snoot. But the actor brought the character alive in a way I don't think anyone else has managed.
If you'd asked me a few days ago this would not have been my choice.
But El Reg and the BBC America Who Hysteria of late have me thinking about it again.