Idea Proposed and Used to Death during the New Series: Monster mashups which, as Arthur Darvill notes in the "Confidential", look sort of like an enormous game of action figures.
Central Premise Recycled From: "The Pandorica Opens," only in reverse (The Pandorica Closes?)-- instead of having a Tesco toy-departmentsworth of monsters ganging up on the Doctor, the Doctor gets a Tesco toy-departmentsworth of monsters to gang up on someone else.
Reference to Moffat's Back Catalogue: It'd be easier to spot the things that aren't references to Moffat's back catalogue. Small children who are special, timey-wimey, the Doctor meeting yet another small girl who will grow up to get jiggy with him, everybody in the universe knowing who the Doctor is, creatures in monks' robes with funny heads, girls with guns, militant Anglican monks, parenthood/couplehood issues, a nursery-rhyme-style poem...
Amy Screws Up the day with Wuv: It's true; those Flesh copies are so good even a mother can't tell the difference.
Joss Whedon Called...: He'd like you to know he's got the corner on Blake's 7 references. Also Rory remembering his time as a Centurion even though it didn't happen in this universe is far too much like Xander's having memories of serving as a soldier even though they didn't actually happen.
And from Lawrence Miles: UNIT-type military organisation with a thing against the Doctor, the idea that time travel affects people's DNA, struggle by various groups wanting to weaponise a time traveler who can't really fight back.
Murray Goldwatch: Much as usual.
Nostalgia UK: The retro Doctor Zhivago-style outfits on the future soldiers.
Inside Jokes: One of the many abortive Doctor Who movies had the Doctor dressing as a woman to defeat Jack the Ripper. The Doctor is also evasive as to whether he's had children.
Teeth! And Hooters! And Honkers! All on the Silurian!
Hats! Sort of, mostly Hoods! though.
Fish! No, they're taking a break this week.
Small Child! Um... pass.
Item Most Likely to Wind Up as a Toy: Eyepatch Lady of course, though while you wait you can go buy some desert-camo Action Men and make your own militant Anglicans. And I'm still holding out for a nine-inch River Song with her own line of outfit and accessories, and adding to that a cross-dressing Silurian with Hooters, Honkers and her own lesbian lover for accessories.