In season 8 episode 1, when the Doctor encounters the episode's villain(s), he keeps saying that this is all very familiar to him, but he can't quite put a finger on it. Is this a case where the audience is supposed to know more than the Doctor (like when he can't keep Clara and Strax straight), or is he referring to something we (the audience) haven't seen yet? As in, are the serious Whovians yelling at the screen, "it's [insert name of classical Dr. Who villain here]!", or are they as puzzled as the Doctor is (and I am)?
At the end of the episode, there’s a throwaway line which hints at the explanation: the ship is called the SS Marie Antoinette, the sister ship to SS Madame de Pompadour.
This was a ship which featured in the Tenth Doctor episode The Girl in the Fireplace (2006), in which clockwork robots were trying to repair their ship using the body parts of the human crew, in much the same fashion as the cyborg in this episode. That’s what the Doctor can’t quite remember, presumably as a result of recent regeneration.
That was the third episode written by Steven Moffat (as a guest writer), who’s now the showrunner and wrote Deep Breath.
He is referring to the 10th Doctor episode "The Girl in the Fireplace", in which clockwork service robots are attempting to repair their stranded space ship with human body parts.
Speaking only for myself, seeing the clockwork automata gave me a sense of deja vu - I knew I'd seen them somewhere on Who before, just couldn't place it. As soon as the artifact with the ship name was shown, it came together for me, although I confess that I hit the PVR pause button and searched up the episode to reaquaint myself with the earlier story.
The Doctor, who normally has encyclopedic (galactopedic? cosmopedic?) knowledge, and staggering powers of recall, was obviously still reassembling his mind after the regeneration, so couldn't quite fit the pieces of this mystery together right away. That gave us, the audience familiar with his past adventures, a chance to "get the jump on him" by recognizing the villain before he does. I suppose that any viewers newer to the show who had not seen "The Girl in the Fireplace" would feel a step behind. I suppose it was a bit of geek-fan-service to reveal the villain to us and The Doctor in that way.
For what its worth, we do often (not always) get to see and identify the villian before The Doctor does (The Doctor asks a question along the lines of "who could be masterminding this situation?" - cut to a shot of Dalek saucers swarming through space). When he's at his best, he usually identifies the Big Bad pretty quickly; much of the time, he already seems to know all about it, even if it's totally new to us.
In addition to the Girl in the Fireplace reference, it may also be the fact the Peter Capaldi had a role in a David Tennant episode where he actually met The Doctor.
Or rather, The Doctor met a man who looks remarkably like one of his latwr regenerations, so when he sees his face in the mirror, it looks familiar.
Peter Capaldi also had a role on the spinoff show Torchwood, leading Russell T Davies (the showrunner in the Nine/Ten eras) to come up with a theory to explain his appearance in both shows+times. Supposedly ince he was hired, Moffat (the current showrunner) called up Davies and asked him if the theory was still valid and Davies confirmed that it still worked.
So we'll see if that plays a role in the rest of Season 8.