Slight tangent here but I was really disappointed when I learnt that Doctor Who Tom Baker wasn't the Tom Baker that used to hang around with The Doors and apparently got them into a lot of the trouble Jim Morrison got blamed for.
Used to love that story (and indeed telling it) so was gutted. To bring it back on topic he's my fav as he was my first and so defines what The Doctor should be to me. Matt Smith is close behind.
I'd possibly go...
Tom Baker
Matt Smith
William Hartnell - love the grumpy
Peter Davison - like Matt Smith an age that defied his looks, though lacked the alien
Patrick Troughton
Dave Tennent - would have been higher but as people said over egged it at the end
Colin Baker
Christopher Eccleston
Jon Pertwee - I know I know but he just seems so unDoctorish to me. I guess as Tom Baker (my Doctor and hence my definition of what a Doctor should be) took over from him he tried to make a departure from what Jon P did and hence that leaves Jon P very unDoctor like to me. Strange as he's in some of my fav stories too.
Sylvester McCoy - Don't care what people say lots of his 'classic' stories are actually a bit rubbish and he just didn't have to chops for me.
I've not rated Paul McGann as I've not watched him in the 'movie' for an age so find it hard to remember what he was like.