Sadly, Steven Moffat didn't get his wish. The celebration of 50 years of Doctor Who contained no references to the strange spin-off Doctor played by Peter Cushing in the '60s. However, Moffat's words do possibly clear up one of the great faux pas in the show's history.
First, some background. Peter Cushing played a version of The Doctor in two films in the '60s. These were Dr. Who and The Daleks and Daleks' Invasion Earth 2150 A.D. The films, which were actually the first Doctor Who to be colorized and the first presented in widescreen as well, were meant to capitalize on the huge popularity of the Daleks and possibly make some inroads in America, where Doctor Who was still completely unknown.
The first film was more or less a remake of the second William Hartnell serial, "The Daleks." At this point it is impossible to overstate how popular the Daleks were, in many ways overshadowing the rest of the show entirely. Terry Nation, the creator of the Daleks, agreed to license his most famous creations to be adapted as long as longtime script editor David Whitaker (author of the novelization of "The Daleks") was hired to adapt.
The films featured a much different Doctor from the one we currently know. First off, he is entirely human. Barbara Wright is no longer his granddaughter's teacher, but another granddaughter of The Doctor himself. Ian Chesterton becomes Barbara's boyfriend, and it is he who sends the four to Skaro when he accidentally activates The Doctor's latest invention, TARDIS.
Otherwise, the plot is much the same as in "The Daleks," and if the film isn't exactly better than the television serial, it is at least no worse. William Hartnell was thoroughly annoyed at being passed over for a film credit for Peter Cushing in the role, but Cushing was seen as a better known face to the cinematic world and therefore more capable of launching The Doctor to a wider audience. He does play the part with more warmth and childish humor than the famously grumpy Hartnell, and is for all intents and purposes a fantastic Doctor.
Except they don't really call him that.
This is one of the few times in the course of Who history that the character is definitely referred to as Dr. Who. He's almost never called The Doctor. "Who" is his last name (His first is never revealed in either film or the rare appearances Cushing's Doctor has made on the fringes of the expanded universe).
Cushing himself always maintained that his Doctor was a proper Doctor, though not necessarily the First as he was so clearly based on. In his mind, the Dalek films represented a future incarnation of The Doctor forced to relive previous adventures by a foe like the Celestial Toymaker. Actually, that's a pretty good idea. Someone should get on that for Peter Capaldi.
Cushing's theory aside, it's long been held in fan theory that Dr. Who is not as proper part of the lineage of the Time Lord. Instead, the hypothesis goes that the Dalek films actually exist within the context of the show. Possibly they are based on stories told by Ian and Barbara after they ceased traveling with the First Doctor, making their way onto the silver screen in mangled forms from the true ones. Moffat's plan to include posters of the Dalek films in the black archives lends considerable weight to this theory.
It also clears up the only other time The Doctor is ever referred to directly as Doctor Who in the course of the regular show.
This story continues on the next page.
"The War Machines" is a brilliant story I highly recommend, and not just because it introduces my favorite companions, Ben Jackson and Polly Wright (no relation to Barbara). In it, the First Doctor and Dodo land in 1966 London at a time when a supercomputer named WOTAN (Will Operating Thought ANalogue) is being brought online in order to help guide the world to a perfect model of logical thought.
Of course it went insane and tried to wipe out humanity. What were you expecting?
Throughout the story, WOTAN wants access to the mind of The Doctor, and repeatedly cries out that "Dr. Who is required." This is the only time that The Doctor is ever explicitly referred to by this name in the course of the show.
Generally this is seen as just a misfire. Many Doctors have been referred to as Doctor Who in the credits over the course of the show, and even if the scripts didn't call him that, the press and the public at large certainly did. Even today, the practice of calling The Doctor "Doctor Who" is considered appropriate when you establish who you are talking about to an outside audience ("Peter Capaldi to be the Next Doctor Who" for example).
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What if it's not, though?
"The War Machines" was released and takes place in July of 1966. Dr. Who and the Daleks was released in 1965, a year before WOTAN came online. With access to all the world's data, isn't it possible that the computer confused the two? After all, Cushing's Doctor is based on and in many ways identical to the First Doctor. All the hallmarks are there: time travel, the Tardis, even the names of known associates. Plenty of films are based on real life; why would it be outside the realm of possibility that the insane supercomputer in its quest to take of the world wouldn't confuse the cinematic hero with the real thing that was Dr. Who's inspiration?
Moffat's intention, sadly unexecuted as it turned out to be, pretty much establishes the Dalek films as real things in The Doctor's universe. Because of that, we can assume that the reason WOTAN, connected throughout the Earth's information field as it was, referred to The Doctor as Dr. Who was simply a misunderstanding confusing two very similar heroes of time.