I always struggle to have one favourite anything, but:
Jon Pertwee comes first - loved his dashing style, the lovely courtesy, the cloak... *sigh*
Then probably Peter Davison - he had a hard act to follow in Tom Baker and his Doctor is a sweet character with a tough centre who I found very appealing
Bakers Tom and Colin and Sylvester McCoy come next - TB became a bit of a parody of himself eventually, though there are individual stories in which he's brilliant; enjoyed both CB and SMcC's interpretations though feel they're both sold short by the way their time in the role was truncated.
Then Paul McGann and David Tennant (sorry, David!). Wish PMcG had been given the chance to do Who properly - one dodgy film just wasn't enough. And whilst I *love* DT's energy and fire in the role I got really fed up with his melodramatics. Partly RTD's scripts, I'm afraid, and DT shouldn't be carrying the can for those, but there it is... again, there are individual stories in which I feel he excelled, but others... oh dear!
Patrick Troughton and William Hartnell I've seen only odds and ends of in the role. Suspect I would really take to Troughton if I'd seen more, but haven't the spare cash for the box sets at the moment!
Puting Chris Ecclestone at the bottom... I never really bought him as the Doctor, which is a shame cos I think he's a brillaint actor.
And I've left Matt Smith to one side this time, as I think it's unfair to judge him one one very recent series. He has the potential to be right up there for me - love his portrayal in S5 - but I prefer to let a bit of water go under the bridge before I make a call.