Some quick thoughts that I've had in a Word document for a few weeks now. I'll post a Top 10 Who episodes of the new series list, seasons 1-6, when I get around to it; however, failing that at present, here's just a few things. SPOILERS BEWARE.
-Steven Moffat really likes presenting his characters with two choices, both of which are ultimately false (See: "Amy's Choice", "The Almost People" (in the case of Jenny), and arguably "The Girl Who Waited"; Rory has to choose one or the other Amy, but it turns out the choice was made for him anyway.
-He's also run the scenario twice where the Doctor brings two opposing groups to the negotiating table, ready to talk peace, only to have an unexpected murder spoil everything and nearly provoke a war. ("The Hungry Earth"/"In Cold Blood", "The Rebel Flesh"/"The Almost People".)
-Moffat and Davies have each run a scenario with galactic policeman trying to capture an escaped intergalactic criminal, who are willing to sacrifice human life to capture that criminal (or are indifferent to it). ("Smith and Jones", "The Eleventh Hour")
-Turning ordinary objects/situations into something science-magical/frightening. ("Gridlock" and "The Idiot's Lantern", not to mention the TARDIS itself.)