Idea Proposed and Used to Death during the Classic Era: Doubles. Particularly of the Doctor. The Chase, The Massacre, Meglos, Mawdryn Undead (sort of), Black Orchid (sort of), Arc of Infinity...
Central Premise Recycled From: There's one hell of a lot of Alien: Resurrection in this one; the monster-Jennifer chase down the corridor is pure homage, but the tough female leader with a secret terminal illness and the whole alien-or-human identity crisis. Setting it in a monastery also recalls the religious subtext to the story (when properly done, that is, not the bowdlerised cinematic version). Androids, or something like them, which are indistinguishable from humans. Plus the idea that the Company is up to something deeply unethical that needs exposing.
Reference to Moffat's Back Catalogue: Small child, asking "where's my father?"
Amy Screws Up the day with Wuv: The last five minutes are one serious Screwup with Wuv, though how, and what the Wuv involved, are for the cliffhanger.
Joss Whedon Called...: He wants back his surprise twist where it turns out one of the main characters isn't who or what you thought they were (q.v. Dollhouse, or am I stretching this one too far? Don't answer that).
And from Lawrence Miles: A woman who drops her jaw and swallows a man? Sort of like the TARDIS in Alien Bodies.
Murray Goldwatch: Strike up the bland!
Nostalgia UK: That mock-regeneration sequence bit, arguably.
Inside Jokes: Ben Aaronovitch once wrote a Virgin novel called The Also People. The Doctor's greatest-hits riff on his own past incarnations mirrors Logopolis; although "Reverse the polarity" and "would you like a jelly baby" are too cliched to be inside jokes, Hartnell's "one day we will return" is just obscure enough to count.
Teeth! Jennifer's got quite the mouth on her.
Hats! No, shoes! are cool this week. Also eyepatches are undergoing a revival.
Fish! No, though the fish and chips remark from last week gets a revisit.
Small Child! Wee Adam, the five-year-old boy who is willing to spend ten minutes on the phone waiting for his Dad to get done murdering himself. Plus an incipient Small Child in the last five minutes of the story.
Item Most Likely to Wind Up as a Toy: I was originally going to predict a limited-edition Amy Pond Possibly Up the Duff (same as the regular Amy Pond figure, only it comes with one of those little red-blue positive-negative icons), but now it looks like we just might get the Amy Pond in Labour playset, so I take that back.