Quick response off the top of my head:
The Mythmakers. No-one ever really talks about this serial (it's missing but so are many other more discussed ones) but I think it's seriously good. Obviously I know it only from the audio but it happens to be one of the best missing stories to listen to in that way as it is scripted very much like a play anyway. With the exception of the Trojan Horse prop (by historical account not very good anyway, although I like the still pictures of it) it is petty much dialogue rather than action.
It's very, very funny, matching the much lauded City of Death for wit and is an actual comedy, perhaps the only one in Doctor Who history to be PURE comedy, as both the Romans and the Gunfighters (and Love & Monsters) have some purely dramatic strands to their storyline (Ian's enslavement in the Romans for example and the shoot-out n the Gunfighters). The nearest the Mythmakers comes to being serious is in Vicki's romance with Troilus.
It's written by Donald Tosh who is one of Doctor Who's most talented writers. In his day he was a pretty significant, even high brow dramatist. And that shows in his scripts, particularly this one.
There's a wonderful sensibility to the whole thing. It just assumes we know about Greek history and will get the jokes, the references, the settings. How wonderful is that in this age where classical knowledge and education is non-existent in the general population. That was part of our culture once. Now, the doctor Who creators deliberately give us cartoon vikings because it's assumed we can't cope with anything more more. Thanks a lot Moffat, you patronizing @£$%. Nice to know they consider their audience to be simple-minded and unintelligent. it will sound petty to most, I'm sure, but they hurt my regard and affection for the show just a little bit with that episode last series. To admit that they dumbed down is shameful.
But I digress... the Mythmakers is a great example of all the strengths Doctor Who (and popular culture in general) does not have in the modern age.
An unearthly Child - the Caveman episodes! I think they're wonderful. I don't understand the low regard people have for them and so am forced to maybe think it is a case of pearl before swine (I can feel it getting hot in here :P). Anthony Coburn is a fantastic writer. 100,000 BC is dramatic, at times frightening, thoughtful, exotic, surreal. The theme of the tribe's search for fire and the power struggles that play around it is fascinating. I daresay there hasn't been a better example of the theme of political factions in conflict in the show's history, and it's been pretty common ground for the show.
Are there many more generally unsettling sequences in Doctor Who than the fight to the death between the two would be tribe leaders in the cave of skulls and the travelers horrified reactions.
And the coup de grace: the travelers escape without helping or resolving anything! They simply escape with their lives and are glad to do so. To some, tied to the show's modern format and unable to accept divergence this is probably a mark against the story but I love the realism of it, the nihilism. The only other serial that does this is the Caves of Androzani (no coincidence: another all-time favourite of mine) and even in that the Doctor is at least heroic in his efforts to save Peri. In '100,000BC' heroism is hard to find, and isn't that somehow fitting for a story set in a period of human history where survival is EVERYTHING and there is not room for philosophy or morality?
Again, it's an example of something Doctor Who could not be now, storytelling in a tone the show no longer has any aptitude for. This is why I love all eras of Doctor Who: they have their own strengths and weaknesses, their own unique styles and sensibilities. For all the strengths the modern show has, there are also things it has lost in its dim, distant past, where I'm sure the Doctor would like to leave that adventure from his youth, when he wasn't a hero, so much as a witness.