Odd as it might be since he was from before my time but my favorite Doctor is the original William Hartnell
Mainly since he was sort of an anti hero. He wasn't such a goodie goodie, and yet he still ended up doing good. He was crotchety and gruff, yet had depths to him.
I also really liked Patrick Troughton and Jon Pertwee, they each brought a very different Doctor to the screen. Sadly some of the Hartnell and Troughton episodes are part of the missing episodes. But reconstructions give a little of what was lost. Troughton and Pertwee are tied for my 2nd favorite.
Then Tom Baker comes in 3rd, as the Doctor who I learned of Doctor Who from. He is the classic image of the Doctor for me, and many others out there. Tom Baker was the Doctor that broke into the US market and popularized the show for many of us.
From there I would jump to the new Doctors and say David Tennant is my 4th, and Matt Smith my 5th.
Then back to classics for me, Peter Davison 6th and Colin Baker for 7th.
Christopher Eccleston probably would have been higher if he had done more episodes. I liked his Doctor but just didn't get enough to put him about 8th in ranking.
Sylvester McCoy might have made 8th here, as I really liked his Doctor and acting. However the episodes and writing were so horrible during that era that his Doctor actually slips to 2nd to last just above Paul McGann. McGann is the Doctor I try to pretend didn't happen.
Peter Capaldi would be my 9th choice. He was one I was not sure of when it was announced, but I had hopes for being more like Hartnell. He wasn't and was at the same time. With a mix of old man and rebellious teen. I feel if he had gone on and done more episodes he might be higher on my list, but he decided to leave, and so stays lower on the list.
Jon Hurt just wasn't a long run, so we didn't get to know him, so ranks 10th.
That leaves previously mentioned Sylvester McCoy in 11th, and Paul McGann in 12th for my ranking.
Something I note is a lot of who people like most tends to be who they were introduced to the series with. For many of Gen X age is was Tom Baker. A few it was Colin Baker. Millennials often site the new series Doctors. Usually Tennant or Smith. I am sort of an odd ball having actually gone back and watched the older stuff, and found I liked the older versions of the Doctor more than the one I was introduced to the series.
All in all, the only Doctor I actively didn't like is McGann. And much of that is due to it being a made for TV movie and going off accepted lore for that horrible episode. McCoy I actually like his Doctor and acting, it was just the era of the late 80's that made for such bad TV and writing that really helped kill it for me. And really caused Doctor Who back then to be cancelled. But McCoy himself was actually quite good.