I'm voting for the first Pertwee/TVM logo (I consider them to be the same logo - tweaks don't count). It just seems to be more timeless and, at the same time, more futuristic than the others. I'm glad the BBC has decided to use it for most classic-series related merchandise.
I've nothing against the diamond or neon logos, or the Hartnell and Troughton logos, but they're products of their time. The neon logo says "80s" to me just as much as the Howell arrangement of the theme (why they're using it for all the DVD releases is beyond me).
I've never cared for the McCoy logo. Something about it just rubbed me the wrong way and I was glad to see it replaced by the TVM logo.
As for the lozenge logo of Eccleston and Tennant (and again I'm not paying attention to the minor adjustments made to it over the last few years), I've never been a hater of it. It works perfectly on television, especially with DW now being produced in widescreen, but it looks damn awkward on the book covers. It works OK on DWM for some reason, though.
I'm looking forward to what the Matt Smith logo will look like (it's even money they'll create a new logo, especially if the BBC is indeed planning to refer to the 2010 season as "Series 1" again).
Alex