While there will always be a large, TARDIS-deep place in my heart for Tom Baker, I voted for Matt Smith. His ability to combine and convey most of the qualities of previous Doctors while still given a distinctive performance, coupled with the uncanny way he can project age, despite being the youngest actor the fill the role, puts him in the top spot for me. Plus, he can do joy-verging-on-mania better than anyone. Including Tennant, who he got that particular trait from.
Smith's aren't my favorite stories. Those are mainly in the Baker and Davison era, with a few from the newer Who (ie all of Moffat's and some of RTD's).