Idea Proposed and Used Despite It Being Stupid During the JNT Era: Bringing back a classic monster/villain and retroactively ruining all their street cred.
Central Premise Recycled From: Star Trek. Namely, those interminable episodes where the crew of the Enterprise/DS9/Voyager/Whatever have to thrash out a simplistic diplomatic conflict involving aliens with rubber faces, noses and honkers (who also usually possess a wise elder-statesman type), and usually wind up with some kind of "maybe in a thousand years' time humanity will be ready!" reset button.
Reference to Moffat's Back Catalogue: Companion plus tagalong of the week strapped to a dissecting table by an alien with designs on their body parts: "The Girl in the Fireplace."
Gratuitous Scottish Joke: Quite a lot of Silurians have Scottish accents, but still no one notices.
Amy Saves the Day with Wuv: Amy tries to save the day with Wuv, or at least to remember her Wuv for Rory to keep him preserved, but this turns out rather less than effective.
Tennant Line: The Doctor bleats on about being the last of his kind again (didn't he say a couple of episodes ago that he didn't really want to talk about it?)
Star Wars Bit: If Aleya and Restac are any indication, the Silurians have an army of clone warriors.
Nostalgia UK: Welsh mining villages.
Teeth!: As well as humanlike noses and honkers, Silurians have humanlike teeth. Which is just as weird.
Item Most Likely to Wind Up as a Toy: Those Sea Devil retro-style ray guns would be a nice idea if Character Options ever get into weaponry beyond sonic screwdrivers.
Something Gets Redesigned: The entirety of "The Eleventh Hour," "Vampires of Venice" and "Amy's Choice," which now have to take place sans Rory.
The Crack in the Universe Is: Grafted on to the story for an exciting coda.