Rose: Doctor and/or companions running from explosion (I know, but visually compare the two sequences, OK? You'll see what I mean).
The End of the World: Chips as comfort food; villain playing popular musical number.
The Unquiet Dead: Aliens with little-girl voices pleading to be let into our world, and some Time Lord is mad enough to do it.
Aliens of London/World War Three: New PM, who's been elected while companion's been away, presides over an alien invasion which isn't all it seems; the cabinet getting killed and the public knowing nothing about this; alien attacks on London; return of Mal Loup the American news presenter; montage of celebrity cameos on TV; Ms Rook's mad-eyed strut through Number 10, brandishing her press pass, is disturbingly like Harriet Jones' robotic "MP for Flydale North!" schtick; the government tracking down and arresting the Doctor and companion, courtesy of the companion's mother.
Dalek: Floating attack balls, plus return of old enemy with new name.
The Christmas Invasion: Hotshot new prime minister turns out to be less cop than expected.
Rise of the Cybermen: Population hypnotically controlled through mobile phones; gas mask-wielding villain who reveals his robotic hordes at the end of the story. Villain meets a sceptical President on the tarmac of an airport and later has him killed.
The Idiot's Lantern: More bird names-- and if you look at the back of Martha's television when we see it briefly, you'll notice that it was made by Magpie Electronics (the boy done made good, apparently).
Army of Ghosts/Doomsday: Again with the celebrity cameo TV montage; again with the rift opening up and thousands of alien robot thingies pouring through; again with the brief images of "normal" people being attacked; again with the arrival of something/one who the local populace think are friendly but, gasp, the Doctor knows better.
The Runaway Bride: Floating attack balls.
Torchwood: Nice to know the Doctor thinks they're as dodgy as the viewers do.
Ripping Themselves Off: Let's hope that Lazarus Experiment reference wasn't just gratuitous, and does actually have an interesting payoff. The Doctor also does the aging thing in "Human Nature" (hope they're paying Paul Cornell a lot).
Old Skool Who: The Leisure Hive (the Doctor aging); The Time Monster/The American Telemovie (the Master has a missus); the Master keeps doing Pertwee and Baker references (swaggering around in red-satin-lined black jacket and gloves one minute, offering round the jelly babies the next); The Sensorites (the sky, burnt orange, etc); The Deadly Assassin (in which we get those stupid Time Lord robes; why couldn't they have broken with continuity on that one, please?); The Mind of Evil (the Master firmly established in powerful sociopolitical role and using it); Genesis of the Daleks (Jack's bracelet seems to be used in much the same way as the Time Ring, even down to everyone placing their hands on it at arm's length); the Doctor Who comics (appearance of Gallifrey, plus a solitary black Time Lord); Logopolis (the Master's speech); The Sea Devils (the Master mistakes a children's programme for a documentary); The Curse of Fenric (sudden discovery of dynamite attached to ordinary household object, followed by panicked exodus and explosion); the New Adventures (A "paradox machine"? Ahem).
Everything Else: Star Wars (so, Time Lords are chosen from the general population at age 8 and taken off to an Academy to undergo rigorous psychic and physical testing? And one of them turned into a megalomaniac with dreams of galactic domination as a result of it going wrong? Lucas' lawyers must be going mental right about now); The Hitchhikers Guide to the Galaxy (stare into the vortex and you go mad, unless you're Zaphod Beeblebrox); Captain Scarlet (hang on, what good is an airborne aircraft carrier, anyway?); Marvel's SHIELD comics also feature an airborne aircraft carrier (I never followed the series so I'm going on hearsay); The Omen (psycho demon child); I Claudius (where Caligula goes around hearing the sound of drums, is acclaimed by the Romans as leader before he suddenly turns on them and reveals the extent of his madness, and, guess what, there's even a Derek Jacobi connection). Harry Potter (kids off at a mystical academy, and one goes mental and becomes a supervillain); Quatermass (car driving madly off down urban street at speed whilst being fired on by heavily-armed types); Phantasm (eccentric villain with floating attack balls which suddenly unfurl with knives); Gordon Brown is currently attempting to build a cross-party coalition cabinet for no good reason, but that's probably coincidence.