Well, I've digested, cogitated and deliberated, and the top-to-bottom ratings of series 1 of Torchwood look something like this:
Captain Jack Harkness
They Keep Killing Suzie
End of Days
Out of Time
Greeks Bearing Gifts
The Ghost Machine
I still think on balance that Small Worlds is a better story and a better 45 minutes of television than Captain Jack Harkness, but CJH feels closer to what the rest of the series should have been, whereas SW doesn't really feel connected to the rest of the series at all.
Mind you, I think on reflection the big problem with the first half to two thirds of the series is that the episodes don't feel connected to each other. That's not to say that we got "stand-alone episodes" as was claimed, just that there didn't seem to be any continuity of characters and situation from one week to the next. I've blogged about the Chibnall effect before, of course.
End of Days is knocked down by the last ten minutes, which were absurdly rushed, threw out a promising story in favour of a big end-of-level computer game monster with no build-up whatsoever, and reverted to the "scum" versions of the Torchwood team. But thirty-five excellent minutes and ten abysmal minutes still make a very good episode (cf 2005 Who episode Aliens of London, which had ten excellent minutes followed by thirty-five abysmal minutes).
Taking the last few episodes, which did start to gel as a series, as the echt Torchwood, I've therefore reconsidered the earlier episodes in their light. I enjoyed Countrycide and Cyberwoman as straightforward action/thriller stories, but looking back over the series as a whole they don't seem to fit in, so they end up near the bottom. Day One fits in a bit more, but is rather plain sci-fi tat, so goes below them. Random Shoes is unforgiveably poor and out of step with the overall feel of the show, and remains in last place.