Season 6 implies a new storyline coming up revealing more about the oldest question in the universe and the character Dorium Maldovar makes it clear that the question is:
"Doctor who?"
A friend of mine stated that the actual phrase "Doctor who?" is used less often than "Doctor what?" or derivations of it.
I have not yet had the time to watch all the old episodes, so I simply don't know what's said more often. Can someone help me out here?
The question "Doctor who?" does not refer to the question which is asked most often on-screen. It simply refers to the fact that most people have no idea who The Doctor actually is. In a way, the question is a bit fourth-wall breaking, as to the viewer, it clearly refers to the title of the show, and to the fact that back in 1963 at the start of Doctor Who, we had no idea who he was, other than a time-travelling stranger.
The "oldest question" pretty much refers to the fact that the show's title question has never been fully answered.
I agree with Nellius, but want to expand a bit. "Doctor Who" isn't a term that exists inside the narrative universe, it's just the title of the show for us. So when Dorium yells out "Doctor Who", it's a fourth-wall wink at us, the viewers, but it's also, I think, a hint at the direction Moffat plans to take in the upcoming season.
As Nellius mentioned, the Doctor's origins have been left murky throughout the show. Even in the old series, when the Time Lords and Gallifrey were still around, it was never directly addressed. We know he stole the TARDIS, but not much else.
But in the last two seasons, it seems Moffat's got grandiose plans for his shift as showrunner. It's not enough to have grand finales with time being ripped apart and the universe threatened - that's just par the course for Doctor Who - but he has to go deeper.
He wants to be the showrunner under whom the Doctor (almost) dies. He wants to be the showrunner under whom the Doctor gets married. He wants to leave a permanent mark on the Doctor mythos. The first big step in that direction is in The Doctor's Wife, the episode Neil Gaiman wrote, which brings the TARDIS up as a character in her own right, and hints at new complications - the Doctor didn't steal her, she stole him.
I feel this predicts a focus, in the upcoming season, on the history of the Doctor, on how he came to leave Gallifrey and come to earth and fall in love with humanity. This will probably linked to some in-narrative "oldest question", perhaps related to the time vortex or something along those lines, that will serve as a narrative counterpoint to the extra-narrative question, "who's the Doctor".
There have been hints that the Doctor may have an identity other than the semi-mysterious one that the second Doctor revealed. That he became bored with the Time Lord ethos of staying home on Gallifrey and semi vegetating - the fourth Doctor alludes to the Time Lords studying all of history, but not remembering which century they lived in.
However, there were hints in Sylvester McCoy's Doctor that he was someone/something other than just good old Theta Sigma, frat boy. When he faced the Gods of Ragnarok, they claimed that they knew his secret, seemingly they knew of him in the "old times" (implication that he was someone else and played a major role in a previous universe).
I am not sure if it was this episode, but in one of the seventh Doctor's final season, she asked the Doctor "Who" he really was. Of course, he doesn't answer.
That the Doctor had another, darker identity has been speculated about before... that he was involved with Omega/Rassilon in the earliest days of Gallifrey... or that he was the original foe that defeated & imprisoned Fenric.
There is a moment early in the series (I've never been able to find it when looking, but I have a clear memory of it; perhaps from an "alternate take") where the Doctor answers, "Caligari." But, since William Hartnell had a way of laughing even while he was serious, it's not entirely clear -- "in-universe" -- how much he was joking.
If one attempts to comprehend the series as a whole, the very insignificance of this extemporaneous muttered quip, forgotten in the selenium past, suggests (to my mind, at least) an eerie significance.
If the Doctor were a sleeper, lucid, avatar of his own larger self, all of his powers are explained. The recurrence of themes like dream-weaving, virtual reality, perception filters, charactes like Daleks, Cybermen, Dominators (Sontarans). Mathematically, all infinities are equal to each other. As Yoda says, "No difference; only different in your mind." Dimensions are relative, right? But relative to what? To the synthetic unity of apperception, subject to the receptual conditions of time and space (thus spake Kant). In a fiction, the apperception of the auditor is functionally projected upon the protagonist (one "identifies" with the hero). The quest of the dreamer is always to discover his or her "true name," upon recollection of which one instantly awakes.
Also, the relativity of time allows one to return to any point just after they last left (as Farscape tells us, "It's going backward that screws the pooch."). So just as soon as the Doctor remembers what he came for, what he's supposed to do, he may yet return home to the Time Lords (they existed then, right? and he remembers them. It has been shown to us that these are the necessary ingredients to "bring something back"), perhaps picking up Susan Foreman (named after the scrap-yard in Ep. 1) along the way; And then, of course, becoming the Valeyard.
So what I'd like to see as the crowning of the series is the real backstory. The Prequel, Prologue, Intro. What's he running from?
The Nothing?
The phrase / question was first used in the second episode of the series. Ian asks The Doctor to open the doors of the TARDIS, addressing him as "Doctor Foreman". The Doctor responds in a mutter to himself.
Eh? Doctor who? What's he talking about...?
Later in the episode, Barbara refers to him as "Doctor Foreman" and Ia corrects her.
That's not his name. Who is he? Doctor who? Perhaps if we knew his name, we might have a clue as to all of this.
In both cases, It's a set-up to the fact that his actual name is a mystery.
Later in the Hartnell years, the name is used literally (albeit accidentally) in The War Machines, when the supercomputer WOTAN says "Doctor Who is required".
That actual phrase is not used in the show itself, terribly often until the new series. Once it began to be used, it became easier to do wry spins on it, like Bill Potts saying "Doctor Wot?" instead. It the same way that they'd make flips to the classic "It's bigger on the inside" line.
For many years, use of the phrase "Doctor Who" was used more on other shows and films, making wry allusions to the program. For example, in Carry On Screaming...
Doctor Watt - Allow me to introduce myself - my name is Doctor Watt.
Inspector Bung - Doctor Who?
DW - No, that's my cousin.
As with the plays on the phrase, once it was being used on the show, it opened the door to address it as an actual plot point, hence the mysterious "First Question".
