OK, here's my best-to-worst. I liked mostly all of them, with some specific exceptions.
Fifth: The Caves of Androzani (just perfect, and for every reason imagineable - only wish the cave monster was convincingly done, or that it was retouched for the DVD release)
Eighth: The Night of the Doctor (basically, CoA on steroids! perfect exit for the Eighth, with a suitably sweet acknowledgement of his extended lifetime via Big Finish's audio dramas)
Second: The War Games (a couple of episodes too long in the middle, but still very good, and Troughton really did get to shine through in this complex storyline that broke new ground while still ending the iconic B&W era)
Ninth: Bad Wolf / The Parting of the Ways (a great two-parter, and the great regeneration story of NuWho, let down by the game show bits - but not by much, I watched the Greek version of The Weakest Link when it was on, so I enjoy them nostalgically still)
Twelfth: World Enough and Time / The Doctor Falls / Twice Upon a Time (what a fantastic exit for the Twelfth Doctor, going against two incarnations of the Master, an offshoot of the Mondasian Cybermen, and before his end meeting with his earliest self! wonderfully emotional, tonally consistent, and easily Moffat's most rewarding, collective experience in years)
Tenth (Meta-Crisis): Turn Left / Stolen Earth / Journey's End (a fantastic finale for series 4, a real mega epic with crossovers with Torchwood and the Sarah Jane show, with the Meta Crisis aspect of it being the only real odd turn-off - but it works still, even without the superb Turn Left)
Sixth: The Brink of Death (for an audio story, and not even a traditional four-parter at that, remarkably effective, as Old Sixie rushes over to save himself, and indeed the Time Lords from the Valeyard, willingly killing himself to prevent his total victory, a real stupendous story that Nicholas Briggs should be proud of, and a solemn but fitting, not to mention proper, goodbye to Colin Baker's much maligned Sixth Doctor)
Eleventh: The Time of the Doctor (a little rushed, some annoying revisions and an over-simplification of facts, but it still moves me with its frenetic pace and genuine emotion - Matt Smith also totally sells it, extremely well)
Tenth (actual regeneration): The End of Time (a bloated mes, yet it still is moving and even heartwarming whenever Tennant and Cribbins are on-screen, and of course the amazing last 30 minutes basically salvage most of it, if barely)
Three: The Planet of the Spiders (its a lot like TEoT, in that its largely self-indulgent parade of tropes reminiscent of the Pertwee era, but at the same time, there's a heart in this and a genuinely nice twist of the Doctor basically instigating the entire story, and essentially his engineering his own death, because of his own ignore due to thirst for knowledge - and such, it could've been better as a shorter feature, but it does still work, Pertwee having maybe the most understated regeneration scene of all time)
Fourth: Logopolis (good plotting, weak characterization, its basically three OK episodes, let down by a rushed fourth episode - still worth it though, for Tom Baker's last proper appearence as the definite article)
Seventh: Enemy Within (it looks great, and its heart is in the right place, but the story is a real mess - thank goodness for McCoy and, especially, McGann, for making the least bit watchable)
First: The Tenth Planet (shockingly, I pretty much don't care for this one, mostly because Hartnell himself gets to do almost nothing for the entire story, which is sad cause he deserved to have a little more involvement in his last-ever story in a show that he starred at and brought millions of people, including most children, with consistent ratings and popularity - still, the Cybermen have rarely been creepier since, and the Doctor's final stand is memorable for all the right reasons)
And an honorable mention for the Warrior and his The Day of the Doctor (a really, really great story - but the Ninth is sorely missed, and McGann should've been in the War Doctor's place). I'd probably rank it below Bad Wolf, really.
