With 50 years plus of canon to pick from, this list by necessity has to be divided into subcategories. It's also not a "best of" list, and highly subjective.
1: First Doctor: The Aztecs. Boringly predictable of me, I know, but Barbara is awesome in it, the Doctor/Cameca scenes manage to be quite endearing, and I approve of those stories where a later regeneration looks up Cameca. It’s also a superb example of DW doing a historical with the Doctor and friends being the only sci fi element in it.
2: Second Doctor: have not seen nearly enough (well, of what still exists) to make such a choice, but between The War Games and the restored The Invasion, I’m going with the later (it’s not as heartrendering, I like the animation of the restored parts, Zoe and Isobel are love, and Vaughn is among the most repellent and efficient human villains.
3. Third Doctor: Here I have to provide one serial for each of his companions (It’s also that I love the era very much indeed.)
Liz Shaw: Spearhead from Space: the show does its first soft reboot, Liz is superb in her first appearance, her prickly dynamic with the Brig is great, so is the Brig’s with the Doctor, the Autons are creepy, and in terms of post-regeneration stories, Jon Pertwee does a neat job of early on suggesting still a lingering bit of Second Doctor mannerisms before settling on the Third Doctor’s personality. There are so many moments I love, but to name just one: the Brig immediately (correctly) deducing the Doctor is lying to him and intending on hightailing it out of there with the TARDIS. He knows his Doctor, all of them.
Jo Grant: Mind of Evil. Not just because it gives the lie to the „all Jo Grant does is scream and ask the Doctor what is happening“ magnificently (Jo in a prison full of criminals holding her own = awesome), but also for some of the best classic Who Doctor/Master moments (and Delgado sublime), both on the funny and the darker side of the spectrum. The Doctor’s reaction when the Brigadier shows up in prison is another classic, too.
Sarah Jane Smith: Invasion of the Dinosaurs: because it’s wonderfully bonkers (the Brig and the Doctor driving near at a dino (or was it a brontosaurus?) being a case in point and very Doctor-ish, and Sarah Jane is still very much in reporter mode in this first story after her original introduction.
4. Fourth Doctor: Err. I always feel guilty for saying so, and yes, I did watch several from several eras (Sarah Jane, Romana I, Romana II, and the very end with Adric; I only missed out Leela episodes so far), but I just can’t warm up to this era. I can see why other people like it so much, but you know, if your first Fourth Doctor story is City of Death and you still don’t feel the love, there was probaly little hope for the rest. So I would pretend if I named anything here.
5. Fifth Doctor: Here I’ll swith mediums for the first but not the last time, because I love several of the Big Finish audios for Five so much more than the tv episodes:
„The King Maker“ for being a hysterically funny spoof both on Richard III theories (I say this, being a Ricardian myself), and on Shakespeare authorship theories, and for still providing some good character stuff - notably the scene between Peri and Erimem in the Tower where they contemplate death which showcases that Erimem, as an ancient Egyptian, is genuinely different from a 20th century person like Peri in a way that satisfies the history lover in me. Also, their friendship rules.
„Fanfare to the Common Man“ - one of the 50th anniversary audios featuring the Fifth Doctor and Nyssa as well as a couple of musicians from Liverpool who also had a thing going on in 1963. It’s clever, funny and eminently listenable whether or not you’re a Beatles fan. Also, separating the Doctor and Nyssa allows Nyssa to land in the Hamburg era of Beatles history, which clearly is better than the Doctor having to go through an ear-splitting stadium and then the Maharishi experience. 😊
6. Sixth Doctor: Audio time once more! The Marian Conspiracy for introducing Evelyn Smythe, 60-something historian, whose dynamic with the Doctor is wonderful, and for the use of Mary I. Tudor as someone who truly believes she’s saving her people even while condemning a great many of them to death - as someone the Doctor relates to.
The Condenned: for teaming up the Sixth Doctor with Charley Pollard after her run with the Eighth and thus creating an intriguing new dynamic while also introducing my favourite female Manchester D.I. (Patricia Menzies) as a guest star (who also has a great dynamic with Six).
7. Seventh Doctor: TV: The Curse of Fenric. Not just for the emotional climax featuring the Seven and Ace dynamic at its most intense and screwed up (in the big climactic scene near the end), or the much earlier lovely moment where his own faith is revealed to be in his Companions - all of them, not just the one with him or the one from his era -; no, also because this has to be one of the most unusual WWII era stories not just DW but a British medium ever did. Instead of Blitzkrieg spirit invocations, we get a British pastor tormented by the bombings of German cities, instead of heroic American allies, there are heroic Russian allies. Oh, and Ace gets to deal with her mother issues, somewhat.
Audio: A Death in the Family. Featuring Ace, Hex (an Audio only Companion) and Evelyn Smythe, with the villain being one of the creepiest the audios have come up with. Evelyn is mainly a Sixth Doctor Companion, but she has some great moments with Seven as well, starting with his cameo at her bedside in the Sixth Doctor adventure „Thicker than Water“, and continuing here, because her position of having known him in different eras of his lives gives her also a different position from which she makes him confront his decisions. But to me, this is primarily a fantastic Ace story, as she has to become essentially the Doctor for the majority of it, and it’s both awesome, heartbreaking and slightly terrifying.
8. Eigth Doctor: Well, here it has to be Audios, because, well, the movie. (And Night of the Doctor was neat but doesn’t really qualify.) I’m currently favouring The Rulers of the Universe, which is the fourth story in the third „season“ of „The Diary of River Song“. It manages to pull off a not-continuity-spoiling team-up between River and Eight, and they’re both splendid here.
Not having had the chance to hear the War Doctor audios yet, I cannot therefore name one of them, but I’m glad they’re still waiting for me, as I really liked John Hurt in the role.
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9. Ninth Doctor: The End of the World. If Rose re-introduced the show, introduced Rose the character and her background , with the Doctor being basially the man of mystery making brief appearances, The End of the World , the second episode, was the one which for me really introduced us to him as a character. Eccleston gets to show his range here, from quiet scenes like the one with Sabe to coldly, lethally angry with Cassandra, and with Rose from joyful to challenged/exasparated/defensive to joy again. The „I can feel the Earth turn“ speech gets the Doctor’s alien-ness across because of how Eccleston delivers it. And the episode also shows RTD’s ability as a writer/producer to switch between whimsy and angst, camp and suspense in the same episode. The use of Tainted Love remained the most memorable use of a pop song on DW until he combined I Can’t Decide from the Scissors Sisters with the Master.
10: Tenth Doctor: separated by Companion eras again.
Rose: School Reunion, for bringing Sarah Jane back (and giving us Fanboy Tennant and the Doctor becoming one in his expression of joy when he sees her again), using ASH really well as the main villain of the week. And no, I didn’t mind the initial hostility between Rose and Sarah Jane. I would have if it had remained this way through the episode, or if this would have happened in subsequent Companion-Companion encounters. But it worked for me in this particular case because Rose really is still very young, and you can tell this is the first time she realises in ways more than theoretical that the Doctor has a history with people. Note, also, that she's the one reaching out to Sarah Jane as the turning point.
Martha: Gridlock. Yes, this even more than the Paul Cornell two parter, or Utopia, though that’s a close runner-up, or The Sound of Drums (ditto). And not just because the Doctor spends much of the episode with felines, though that helps. 😊 No, it’s everything: Martha having enough of the evasions her and making him talk to her, the general concept of traffic jams writ large both on a literal and metaphorical level, the redemption of Novice Hame (last seen the previous season) - the exchange between her and the Doctor is among my favourite DW moments -, all the quirky characters Martha and the Doctor meet and the society they form. Oh, and I think this is also where one of my favourite Murray Gold melodies first shows up - „This is Gallifrey“ - though it wouldn’t be fully played out until the Master episodes.
Donna: Fires of Pompeji for the Doctor-Donna dynamic in both funny and serious ways making me love this particular Doctor and Companion combination to bits, for making one of the most often depicted events in Roman history feel truly scary for me again, for the way the ongoing turning-into-stone thing visually foreshadows the look of the dead bodies in the Pompej museum, for the sheer nerdiness of the guest family being named after Latin book examples, and for Peter Capaldi making his debut in the Whoverse.
11. Eleventh Doctor: Amy: The Doctor’s Wife, hands down. Doctor/TARDIS OTP, Neil Gaiman’s in top form as a guest script writer, the Amy and Rory scenes when the villain of the week mindmesses with them are creepy and not a little heartbreaking, but Amy also has a hilarious moment early on when in reply to Rory’s „he’s a Time Lord“ she replies „That’s just what they are, it doesn’t mean they know what they’re doing“, and look, I just love the episode.
Clara: The Day of the Doctor, aka the 50th anniversary special. Moffat shows off his fanboyness and timey-whimey-ness with glee, Matt Smith, David Tennant and John Hurt all enjoy themselves a lot (but also deliver on the serious front in the scene where the War Doctor asks how many children died on Gallifrey), Billie Piper is perfectly used as the Moment, the two Osgoods are a great concept, and I don’t have to be a fan of the Fourth Doctor to become putty at the unexpected Tom Baker appearance at the end. „If I was you…“ indeed.
12. Twelfth Doctor: Argh, how to narrow it down? I have so many in that era.
Clara, season 8: it’s a draw between: Mummy on the Orient Express for the great balance between intense and intensely messed up Doctor-Clara dynamic, suspenseful adventure, moral ambiguity of the Doctor and gorgeous 1920s costume. The solution to the central mystery plot, as it were (how to deal with the Mummy) is a very Whovian thing and fits thematically with several other elements of the season.“ And Time Heist for pulling off the heist story concept with great Whovian flair (and actual reasons why this needed to be a sci fi tale), memorable guest characters in their own right whose interaction with our duo also offers great character stuff fort hem, and the way it shows me neat little easter eggs whenever I rewatch.
Clara, season 9: Heaven Sent, aka Peter Capaldi’s tour de force, is hands down one of the best DW episodes ever for me, but I don’t know that I can watch it very often, because it’s also devastating, but… yeah. I love it.
Bill: The Eaters of Light, aka DW does Rosemary Sutcliff - no, not really, but it’s a neat historical in which Bill, the Doctor and Nardole all get good character stuff, and there’s a superb Missy sequence at the end, too.
All the elements that made me love the season, combined! Bonus point for the Romans being presented as three dimensional and not evil and STILL getting called out on their imperialism. (Usually, it's either evil Romans or Empire-as-benevolent-to-all.)
Specials: The Husbands of River Song. River, it turns out, works best for me with the Twelfth Doctor. This is funny, hilarious, tender, our two leads shine, and the final use of „Hello, Sweetie“ is the perfect pay off for several seasons of build-up and turns me into mush.
13. Thirteenth Doctor: with only one season to choose from yet, I’m torn between the season opener which does a great job of introducing both this latest version of the Doctor and the new companions, Rosa and Demons of the Punjab for both their uses of history and the way our gang responds to it. I have to add, though, that while I really liked all three, none of them by themselves have made me love them yet. They’re simply my favourites of the era so far, not of DW in totem.
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