The Unquiet Dead: The Doctor meets, and bonds with, a historical figure despite knowing that something really tragic is shortly to happen to them.
Father's Day: Messing with causality so that someone who should be dead survives, only for them to kill themselves voluntarily.
The Parting of the Ways: The imagery of the Dalek hovering slowly up in front of a window, watched by a girl or young woman. Solar flares interrupting communications.
The Girl in the Fireplace: The Doctor meets, and bonds with, a historical figure despite knowing that something really tragic is shortly to happen to them.
The Satan Pit: Base full of multiethnic people in sensible clothing who are sitting on top of some long-buried nightmare which is about to start slowly taking over and/or killing the crew.
42: Spaceship full of multiethnic people in sensible clothing, who are floating on top of some long-buried nightmare which is about to start slowly taking over and/or killing the crew.
Blink: "Don't drink the water!" as analogue to "Don't blink!"
Utopia: People in a sealed base with a rocket being afraid of some human-like people with funny mouths, one of whom gains access without people realising what she is.
Voyage of the Damned: Doctor attempts technological solution to save companion-figure, with Pyrrhic results; an "insignificant person" saved from the disaster by the Doctor rushes off into contemporary London.
The Fires of Pompeii: This one's so obvious even the programme itself mentions it.
The Sontaran Stratagem/The Poison Sky: Techno-obsessed tragi-comic American nerdboy-- they even look kind of similar, with black hair and goggle-eyes. Freeze-framing the obituary reveals this one's also a boy genius.
Silence in the Library/The Forest of Fear: Library full of multiethnic people in sensible clothing, who are sitting on top of some long-buried nightmare which is about to start slowly taking over and/or killing the crew. Plus the Doctor meets a woman he really, really likes, who then kills herself.
Midnight: Another small group of people trapped in a small ship, in the middle of a hostile alien environment, with one of their number taken over by an alien; they are suspicious of the Doctor, and the situation is finally resolved when one of them commits suicide.
The Stolen Earth/Journey's End: Technically a revisiting rather than a recycling, but still involves a riff on a past adventure.
The Sarah Jane Adventures: Previously had the corner on people who are supposed to be dead getting a paradoxical reprieve and then killing themselves anyway.
Catchphrasewatch: Mostly absent, but Tennant does work a "Molto Bene" in there.
Old Skool Who: "Fury from the Deep" (People taken over by something that makes them go goggle-eyed, big-mouthed and exhaling); "The Wheel in Space" (Space station full of multiethnic people in not-very-sensible clothing who are being sat upon by some long-buried nightmare which is about to start taking over and/or killing the crew); actually, pretty much any of the "base under sieges" of the mid-to-late Sixties for multiethnic crews menaced by aliens; "Remembrance of the Daleks" (Daleks being afraid to mess with minor points of causality when concocting their reality-destroying schemes); Mars is getting pretty damn crowded between this story, "The Ice Warriors" and "Pyramids of Mars" (which also riffs on the whole "is time fixed or fluid?" question); K9 indicates the Doctor's aversion to cute robots is pretty recent; "The Aztecs" (character spared from death by Barbara kills himself anyway); "The Massacre" (it's not OK to save Anne Chaplet from the Massacre, but it's OK to remove her possibly direct descendent from the 1960s); "The Ice Warriors" (the Doctor trapped in an airlock with a person threatening to pump the air out); "The Reign of Terror" (start of the idea that there are fixed points in time which can't be altered); "The Tomb of the Cybermen" (crew debating which of many groups the mysteriously-arrived Doctor may be from); "The Power of the Daleks" (Dalek recognising the Doctor due to events which haven't happened yet).
Everything Else: "Silent Running" (space greenhouses, cute but useful robots and blissed-out hippie space gardeners who dig their veg both literally and figuratively); any zombie movie in which the zombies can run fast (principally "Dead Set" and "28 Days Later," though the "everybody dies" ending of the recent remake of "Day of the Dead" is also in there); "The Thing," particularly the John Carpenter version (isolated research base full of monoethnic people in sensible clothing who are sitting on top of some long-buried nightmare which is about to start slowly taking over and/or killing the crew; the base is blown up to prevent said menace from spreading); "28 Days Later" also is briefly homaged in the shot of the drop of water falling on Roman's eye; Terminator 2 (an explicit homage in the way the water zombies run); Wal-E (Gadget's appearance; Confidential makes it clear the resemblance was originally so strong as to be almost actionable); any anime series featuring a cute robot and/or catchphrase-repeating character (Ulysses 3000 and Science Ninja Team Gatchaman, I'm looking at you); cute robots with catchphrases also feature heavily in both Buck Rogers ("Bidibidibidi...") and the Star Wars prequels ("Roger-roger!"); any Joss Whedon series featuring a comic goggle-eyed nerd ("Dollhouse"'s Topher is the closest IMO); Life on Mars (bad David Bowie puns); 2001: A Space Odyssey (general design appearance, people calling up their kids on videophones).