I have to say, I prefer Matt Smith, primarily because his seems to be the most unique interpretation of the three. Tennant can probably pull off a few of Smith and Eccleston's lines, but I could never see Eccleston pulling off any of Smith's lines. (and yes, I know Gaiman originally wrote his episode with Tennant in mind)
However, I realize that that could be part of the writing itself, in that sometimes Ten was written more as an extension of unfinished business with Nine, rather than his own Doctor. Still, I think Nine and Ten are just a wee bit too similar in many aspects.
With that said, I liked them all, though Tennant was eventually starting to grate on me towards the end. And I would have loved to have seen Eccleston in at least another season. And imagine, just imagine, Eccleston going up against the Silence!