The End of the World (also The Long Game, The Sontaran Strategem, etc.): Character looking down on the Earth from a space station/ship orbiting it, and being amazed.
The Empty Child/The Doctor Dances: The Doctor stalks Rose before she's met him.
The Parting of the Ways: the Doctor absorbs a fatal dose of radiation to save his companion and then regenerates. Also the Doctor faced with a moral choice which involves the possibility of killing one's enemies.
The Christmas Invasion: the Doctor's hand is the first bit of him to start regenerating.
The Satan Pit: The Doctor miraculously survives a fall from a great height.
Doomsday: Participant group in the Time War, believed extinct, turns out to have been hiding itself someplace improbable, and thanks to someone activating the trigger are now coming back in force. They are then sent back to a place the Doctor likens to hell, via the usual machina.
Voyage of the Damned: Ship falls into the Earth's atmosphere, pulls up just before hitting a stately home, while the Doctor shouts "allons-y".
Smith and Jones: the Doctor again absorbs a fatal dose of radiation, though this time he shakes it out through his shoe. Martha Jones' married name is apparently Martha Smith-Jones.
Gridlock: the Doctor jumping through a hatch at the bottom of the ship (though it made more sense in Gridlock; why the hell does a ship like the Hesperus have a hatch at the bottom, which could let in the vacuum?)
Human Nature/The Family of Blood: Device which can rewrite Time Lord DNA.
Last of the Time Lords: The Doctor being wheeled about in a wheelchair, plus getting lots of gay emo moments with the Master.
The Sontaran Stratagem: People saluting the Doctor.
The Doctor's Daughter: the Doctor pulling a gun and then not shooting people with it = "The man who never would" speech.
The Stolen Earth/Journey's End: Planet mysteriously appearing in Earth's sky; when it disappears, one of the companions' mums rushes out into her garden and looks up at the sky. The Doctor sits around in space not knowing what to do. Extended self-indulgent ending involving every single Tennant companion ever, except the ones Stephen Moffat wrote. Bad Guys have a crazy visionary among their number.
The Waters of Mars: The Doctor going on and on about who's important and who isn't.
Torchwood: Glove-based technology.
Who's in the Star Wars Cantina: Hath, Judoon, Adipose, Slitheen, the Graske, a Sycorax, the red-skinned and white-skinned people seen in "New Earth" and "Gridlock", Murray Gold (the song "My Angel Put The Devil In Me" from "Daleks in Manhattan"). And that werewolf fellow from "Being Human," can't think why.
Old Skool Who: "The Ribos Operation" (the Time Lord psychic). "Planet of the Spiders" and "The Caves of Androzani" (both of which involve the Doctor dying through absorbing fatal radiation or other toxin). "Logopolis" also featured a fall from a great height, and it and "The Caves of Androzani" both have visual nods to all the era's companions. "The War Games" (sinister Time Lords, plus the youthful Master's outfit in the initiation scenes). Faction Paradox (the nature of the Time War as described in the opening scene). Vengeance on Varos (the original story featuring the Doctor sitting around for ages not doing anything). The woman in white appearing randomly to Bernard Cribbins = The White Guardian (while speculation as to her actual identity continues, the fact is, she *acts* like the White Guardian does in the relevant stories) or possibly the Watcher. "The Ark in Space" (yet another iteration of the "homo sapiens" speech in the Doctor's conversation with Wilf about the value of the human race); "Pyramids of Mars" (the human race compared to insects). The Seeds of Doom (the Doctor jumping through a glass skylight). The Tenth Planet (planet appearing in Earth's sky). The Five Doctors (appearance by Rassilon). "Silver Nemesis" (cameo by world leader impersonator). "The Twin Dilemma" (villain being attacked by having a vial of fluid thrown at them).
Everything Else: The Space: 1999 episode "Brian the Brain", ironically guest starring Bernard Cribbins (two people in sealed glass booths, one of whom must sacrifice their own life for the other to escape); Star Wars (the "cantina" scene, plus the Time Lords stalking through Gallifrey at the start, plus Wilf's Milennium Falcon laser guns bit, plus see remarks last episode.) The cactus people's ship is called Hesperus, referring to the Longfellow poem, and looks like the offspring of Red Dwarf's Starbug and Battlestar Galactica's Colonial One. Macbeth (a prophecy coming true but not quite in the way its referent expected). The scene where the Doctor points the gun from the President to the Master is too much like the old joke along the lines of "you're stuck in a room with a gun, Tony Blair and Margaret Thatcher; the gun only has one bullet, who do you shoot?" to pass comment (although one hopes Wilf would have put more than one bullet in), Pennies from Heaven's line "the song is over but the melody continues." Babylon-5 (prophecies, plus the Doctor falling from a great height is rather like Sheridan at Z'ha'dum). Matt Smith's speech at the end as he figures out what crashing is, is straight from The Hitchhikers' Guide to the Galaxy (and the whale falling to Earth).