Intresting results from the latest poll in Doctor Who magazine to determine the order in which fans like the 200 stories so far
Those aren't the actual rankings. From DWM 413:
Top 10
01 The Caves of Androzani
02 Blink
03 Genesis of the Daleks
04 The Talons of Weng-Chiang
05 The Empty Child/The Doctor Dances
06 Human Nature/The Family of Blood
07 Pyramids of Mars
08 City of Death
09 The Robots of Death
10 Bad Wolf/The Parting of the Ways
Bottom 10
10 The Dominators
09 Fear Her
08 Paradise Towers
07 The Underwater Menace
06 The Space Pirates
05 Time-Flight
04 Underworld
03 Time and the Rani
02 Timelash
01 The Twin Dilemma
Ranking of Doctors based on story score averages:
01 Christopher Eccleston
02 David Tennant
03 Tom Baker
04 John Pertwee
05 Patrick Troughton
06 Peter Davison
07 William Hartnell
08 Paul McGann 135 TVM
09 Sylvester McCoy
10 Colin Baker
Highest ranking per Doctor
001 Davison The Caves of Androzani
002 Tennant Blink
003 T Baker Genesis of the Daleks
005 Eccleston The Empty Child
014 McCoy Remembrance of the Daleks
018 Troughton Evil of the Daleks
032 Pertwee Inferno
037 Hartnell The Daleks
046 C Baker Revelation of the Daleks
135 McGann TVM
Lowest ranking per Doctor
200 C Baker The Twin Dilemma
198 McCoy Time and the Rani
197 T Baker Underworld
196 Davison Time-Flight
195 Troughton The Space Pirates
192 Tennant Fear Her
190 Hartnell The Space Museum
187 Pertwee The Time Monster
165 Eccleston The Long Game
135 McGann TVM
In general the poll is mixed well. Fans don't appear to prefer one series over the other and both have placements all over the list, including the top and bottom 10. Eccleston has the strongest showing in story averages, but a lot was riding on that season so it makes sense they'd be stronger scripts than usual. He also benefits from having just one season, so there's less of a chance for clangers (his worst story is 35 from the bottom spot).
Fans seem to like the TVM more than is generally believed. They also seem to enjoy the later McCoy stories much more than conventional wisdom would have us believe, with several stories in the top half and very strong showings for Remembrance and Fenric.
Hartnell and Pertwee are solid mid-tier Doctors without many runaway hits nor clangers. Tom Baker and David Tennant have the strongest presence in the top of the charts. Colin Baker is by far the worst performing Doctor.
I believe DWM readers picked Tennant as their favorite Doctor, but that's revealed in 414 and I don't have it yet.