Haven't seen enough of Classic who to make a judgement of the stories of those doctors but from 2005 to now
9th doctor
best - a three way tie between the the three two parters of the series, as i think they are all great but each is so different in tone and style that it is hard to judge them against each other.
worst - I honestly don't have a single story I dislike in that entire series. If I absolutely have to choose one that I could say was weaker than the others, then perhaps boom town. Thats not to say I dislike the story at all, just that out of such a strong run, it probably has the least going on.
10th doctor
Best - The stolen earth/Journeys end - A true masterpiece that has yet to be bettered as finales go, in my opinion. A wonderfully put together story representing a culmination of everything that came before it in 10's era. Lots of companions, davros, daleks, a big threat harsh destruction scenes, emotional scenes, funny scenes, sad scene's, the doctor getting challenged on the nature of his personality. It has everything a good story should have and binds it all together effortlessly and coherently.
Worst - Love and monsters
11th doctor
Best - Two way tie between A Christmas carol and day of the doctor. A Christmas carol was one of the few Moffat examples in his era of timey wimey done well. A new telling of a classic story which just worked perfectly. As for Day of the doctor, what can I say that hasn't already been said many times. Just epic, and a fitting celebration of 50 years. Would have been better with eccleston rather than a one episode doctor gimmick, but is still great as is.
Worst - NIght terrors - Just terrible.
12th doctor
Best - Last christmas - This episode had a good strong story which was clever with plenty of twists and turns, and more importantly frequently felt like it had real peril. Also Capaldi in this episode feels really like he has settled into the role more than any of the episodes that came before, and the usually overbearing Clara even is the co operative likeable Clara that is so rarely seen.
Worst - Forest of the night - seriously I wonder how this even made it past the scripting submission stage.
The caretaker is a close second though. A pointlessly boring episode where it became the Clara show like no other.