Being a list more or less in reverse order of the gutsiest moves ever pulled by Doctor Who production teams over the last half century.
#10. Amy is Pregnant/FleshLet's start with a recent one. The very idea that the Amy we've been following for at least five episodes was a fake (though remote controlled by the real one) was quite the shocker, falling into the category of "everything you thought you knew is wrong". What's perhaps bolder is that they've finally allowed hanky panky in the TARDIS, where a couple of married companions made a baby! Moffat sure likes to lay on the "firsts". One would have thought that Russell T Davies would have beat him to it with all his soap operatics, but it seems RTD may have in fact been too skittish about breaking THAT particular fan rule ("There shalt be no indication that sex hath been had in the blue box.") And with other providers of geeky pop culture apparently of the opinion that audiences do not respond well to married heroes (Marvel and DC, I'm looking at you), there's a measure of bravery in domesticating traveling companions and not forcing them, as the show has habitually done, to stay behind.
#9. Morgus turns to camera in The Caves of Androzani
Though obviously, Doctor Who has been "told" in a number of ways, that's because it's lasted so damn long. The "live play" feel of the Hartnell years only seems different from Pertwee's James Bond Lite because television itself had time to change. The first real directorial shock comes in The Caves of Androzani when a young, maverick director by the name of Graeme Harper has a soliloquy spoken directly to the audience, one of several stylistic touches (another being Sharaz Jek under the table) that take Doctor Who into bold, expressionistic territory. Even though the new series has done video confessionals (Love & Monsters) and comedy flashbacks (The Unicorn and the Wasp), it still has never been this outrageous. I still marvel at how it ever got past John Nathan-Turner.
#8. Dalek cut-away
"Mission to the Unknown" is still the only episode of Doctor Who not to feature either the Doctor, any of his companions, or even the TARDIS. It basically acts as a prologue to The Daleks' Master Plan, but because that story is still 4 weeks away at that point, it seems properly divorced from it. Because there were so many episodes a year back then, the main cast would frequently have to be written out for a week or two as vacations came in, but never all at the same time. What an incredibly ballsy move to go ahead with this. Only the Daleks signal that this is a Doctor Who episode, but of course, they're bankable enough that "Mission" isn't THAT much of a risk. Still much more of a risk than Doctor-lite episodes in the new series though.
#7. The Doctor's first kiss
These days, the Doctor kissing and hugging is so common as to be cliché. Back in 1996 when the 8th Doctor had his first, second and third (above) kiss, it was one of the most extreme changes to his characterization ever attempted. The TV movie failed, so most fans consider its innovations failures as well, but history has shown that a kissing Doctor can bring in viewers. Maybe it just naturally came out of its Hollywoodian script and its crafters thought NOT making him a romantic lead would be the riskier proposition in the U.S. market. Or maybe they knew what they were doing and were resolute in putting their own stamp on the 7-year dead property.
#6. Captain Jack
Continuing in the psycho-sexual vein, the existence of Captain Jack seems as unlikely a proposition to succeed as any. Here we have a gay/bisexual/omni-sexual character, which is unusual enough in itself for television, especially a MALE gay character. Now make him an action hero. Now putting him on before watershed, seducing soldier boys and talking dirty. And finally, make the show he's on one that has traditionally been asexual in the extreme, with organized fandom screaming bloody murder about a kiss or three, for Pete's sake. He even kisses the Doctor on the mouth. How did Captain Jack ever pass fans' litmus test? And yet, I've had straight male fans in my living room who've professed sexual attraction for Captain Jack (little Iantos, all of them). I imagine my friends are 1) mostly joking and 2) open-minded about such things, but nonetheless, Captain Jack was EMBRACED and even got his own spin-off series. Talk about a risk paying off.
#5. The Doctor gets married
Ok, ok, we can't confirm that this is indeed the case, but since we've been allowed to believe the Doctor and River Song are married sometime in his future, it is currently true. And even if it isn't, it's still one gutsy shocker. Kissing is one thing, especially the way it's been approached (either as innocent joy, life-saving trick or unreciprocated surprise), but a deep and intimate RELATIONSHIP? It's a bomb so big, it's been set up years in advance! We've had the entire back half of the relationship (pre-marriage, from the Doctor's POV) to get used to it. It serves the Doctor (and the show) right for going no further than sharing hot cocoa with Cameca (that first year) and making us deny our libidinous thoughts for so long.
#4. The Doctor's exile
Doctor Who is about a time traveler, right? So the production team who oversaw the transition between the 2nd and 3rd Doctors (and between the black & white and color eras) must have been BONKERS to do away with that basic premise! When you watch Pertwee's first season, you'd be forgiven for thinking it's a completely different show (if not for the familar names like Doctor and UNIT). And it is. From Wells' Time Machine, we head into Quatermass territory. Once again, the risk paid off and Pertwee became (and still remains) one of the most popular Doctors ever. The exile didn't last all that long before the Time Lords started allowing the TARDIS to go places from time to time, but it was still a drastic and potentially destructive move to strand the Doctor in a single place.
#3. Time War Annihilation
Aside from the confused TV Movie in '96, we really hadn't had any Who on television for 16 years when it came back in 2005. Different Doctor, different companion, different TARDIS interior, different sensibility. We were expecting that. But the most shocking change made was the destruction of the Time Lords "in between" series. Since The Time Meddler, it was pretty much expected that some production team some time would introduce the Doctor's people. Once they showed up, they became a big part of the show's mythology (for good or ill, you might say), so the last thing anyone was expecting was their erasure from history. The Doctor as Last of the Time Lords became a mythology unto itself, and though they were baggage I far from miss, I still realize how ballsy RTD was to EXPLICITLY do away with them in order to transform his protagonist, not merely streamline him.
One of the very first moves that I can't believe was pulled off is the first regeneration. Think about it! Our lead actor is leaving the show due to illness, what do we do? After all, the show is NAMED after him. Why not just replace him? But they didn't do a Hartnell look-alike contest like they did for The 5 Doctors, no. They allowed a new actor to take on the role and make it his own, creating a tradition that has given us 9 more Doctors since. We've seen stuff like that on long-running soaps ("the part of Stefano will today be played by...") or sometimes to change a Darren, but never with an in-story explanation! It was an incredible leap to make and it's become one of the most exciting things about the Who experience.
#1. An Unearthly Child
Face it, the boldest, most ambitious, most audacious thing Doctor Who ever pulled off... is its first episode. From the strange sounds of the theme tune to the shocking entry into the TARDIS to the mysterious title to the unlikable protagonist to the very premise of people traveling through space and time in a police box that's bigger on the inside... There was nothing like it on tv at the time (nor is there now, arguably). You know, sometimes I wonder how the first person to put yeast in bread to make it rise did it. What accident or intuition led to this discovery we now take for granted. And I wonder the same thing about Sydney Newman and the original Doctor Who production team. How did they arrive at those exact ideas, and how could the BBC go for them. The show's beginnings are well documented, but it still doesn't explain the human dimension. It's crazy to think it would even work, much less for close to 50 years now.
There are runners up, of course, but often they occurred not out of boldness, but out of production necessity (the disappearing Doctor of The Celestial Toymaker, for example) or were accidents (the accidentally rude monsters would have been daring indeed had designers realized what they were doing). The death of Adric is another one I dismissed as remarkably congruous with fans' wishes, but I might have but Katarina's on here had she been a companion for more than a couple episodes. The Daleks' first appearance might be included, but they come so early, it's not like they upended the show's still developing format or anything. Overall, it's surprising how "safe" the show's been given its audacious premiere. It's why I can count the truly bold moments on my fingers. But perhaps I've forgotten your favorite?