There are several Doctors who do not quite fit into the official canon, so which one did Moffat think merited a mention, anyway?
As you may be aware, in addition to the many actual Doctors who have appeared on Doctor Who, there have also been very many Doctor-ish Doctors who appeared elsewhere in adventures who don't officially fit into the established universe. Richard E. Grant, for example, has been the Doctor on two separate specials (Curse of the Fatal Death and Scream of the Shalka), but neither qualifies him as the Doctor proper. Rowan Atkinson, Jim Broadbent, Hugh Grant, Joanna Lumley and a host of actors in various audio adventures have all unofficially played the Doctor.
But none of them were the one Moffat wanted for the 50th.
Peter Cushing was.
Yes, for those unaware, Peter Cushing was the star of two feature films that reimagined Doctor Who for a worldwide audience back in the 1960s. The TARDIS had a whole new set, the Daleks featured heavily, and the Doctor's name was actually Doctor Who. It was weird, but pretty popular. Most importantly, though, Steven Moffat liked those movies, and he would have referenced them in the 50th. Here's the full explanation from the Moff himself:
When I started writing The Day of the Doctor I knew I wanted every Doctor to make some sort of appearance… But what about Peter Cushing? Now I love those movies… but they don’t exactly fit with the rest of the show, do they? … You remember that line, in the Black Archive, when Kate is explaining about the need to screen the Doctor’s known associates… She wasn’t supposed to be looking at the Vortex Manipulator – originally she was walking past the posters for the two Peter Cushing movies. In my head, in the Doctor’s universe those films exist as distorted accounts of his adventures… Sadly we couldn’t afford the rights to the posters.
That's a shame, really. A discount surely should have been afforded. What would have been the downside? I imagine that, had those posters appeared, a number of people would have actually been curious to see those old movies who might otherwise never have afforded them a glance.
Ah, well. Peter Cushing -- you deserved better.
(via Doctor Who Hub)