Sorry to make you wait for this one-- I've been out of town.
The End of the World: The year Five Billion, with its fully-blown nostalgia industry.
The Unquiet Dead: As the script itself points out: famous writer, supernatural adversary, the Doctor gushing away like a fanboy.
Tooth and Claw: “No, no, don’t do that” as companion attempts local argot; dinner party with discussions of the supernatural, lots of chasing of monster and being chased by monster, and goings-on about Britishness.
Smith and Jones: The Doctor neutralizing some kind of normally-fatal poison or radiation through Time Lord physiological magic.
The Shakespeare Code: Aside from the obvious (see The Unquiet Dead, above), running gag about the Doctor and companion giving a famous writer all their best ideas, and speeches about how brilliant writers are, and how the power of writers’ imaginations alone can stop disasters happening (I’ve got five published books to my credit, and yet, somehow, I wasn’t able to stop Boris winning the London mayoral elections).
Torchwood: Mental link between two characters, such that if one dies, so does the other—“They Keep Killing Suzie” again.
Catchphrasewatch: “We’re not married”; Donna gets to tell Agatha Christie she’s brilliant. Christie quotes her own catchphrase about little grey cells.
Good gravy, now they’re even recycling *within* the season: Yet another alien creature wandering around with half its brain somewhere else.
Old Skool Who: The Doctor’s already had a Christie-esque adventure in the 1920s—the strikingly-similar-to-this Black Orchid. There’s a Big Finish involving giant mutant wasps, but I can’t recall the title right now. The Curse of Fenric (Donna telling Christie that everything will be better in the future = Ace telling Rev. Wainwright that everything will be better in the future). The Green Death (giant wasps that can be killed in the same way the little ones are). And of course The Ark in Space (three guesses).
Everything else: Cluedo (Professor Peach in the library with the lead pipe); The Box of Delights (shape-shifting ginger-haired vicar). I’m not much of a Christie fan (sorry—always preferred Dorothy L. Sayers) but apparently if you are, there’s lots of inside references to her books and namechecking of the titles (though somehow they managed to steer away from including the one beginning with the words “ten” and “little”). Brideshead Revisited (young camp noblemen having gay affairs in the 1920s, plus Aloysius guest-starring as the teddy bear). Gosford Park (servants keeping secrets having to do with unplanned pregnancies among their noble employers). The Man with the Golden Arm (character who has been faking paralysis in order to keep their spouse from leaving them, though maybe he got it from Little Britain instead). Raffles (society burglar who infiltrates country-house weekends and nicks the family jewels). The Anubis Gates (the protagonist combats strychnine poisoning by eating the contents of his fireplace, remembering that carbon neutralizes strychnine). The Incredible Hulk (“you wouldn’t like me when I’m angry”). The Prisoner: The Girl Who Was Death (poisoned man drinking a variety of strange things to induce vomiting).
Incidentally, teddy bears weren’t invented until 1902, so, if the room hasn’t been disturbed since 1886, then Lady Eddison has a pretty avant-garde toy designer in her employ.