Aliens of London/WW3: Not just Harriet Jones still clinging psychotically to her ID-card routine, but slightly unbelievable antics using the Internet.
Dalek: Crazy Dalek in chains, plus one of the traditionally cited defenses against Daleks (running upstairs there, covering the eyestalk here) scotched by new Dalek technology.
The Parting of the Ways: "Ladies and Gentlemen, we are at war!" Plus the obvious stuff about Daleks invading Earth, shots of flying Dalek armies descending, Dalek creators generating whole Dalek armies out of nothing. etc. Woman firing machine-gun at Dalek while screaming.
Rise of the Cybermen/The Age of Steel: Robot creatures that are herding humans together for some purpose. Plus the wheelchair-bound mad genius thing comes full circle. Secret sending of mobile numbers.
Army of Ghosts: Aliens land and start going into the streets of Cardiff kidnapping nuclear families.
Doomsday: Daleks led by a lateral-thinking leader; barriers between universes breaking down.
Smith and Jones: Not just the Judoon and the disappearance of a seemingly unmovable object, but the return of the "no blow fo ro mo'fo" dialogue.
Daleks in Manhattan: More invasions by lateral-thinking Daleks, and Daleks getting a hate-on for one of their own that's a bit different. Plus some Daleks in Manhattan (what do you want to bet the Empire State Building got blown up first?)
The Sound of Drums: Lots of crazy mobile-phone antics, and teleport-device escape routes, plus ex-companion guest stars.
Last of the Time Lords: Not every single person thinking "Doctor" at the same moment, but every mobile phone on Earth ringing him at the same moment.
Torchwood: Creative use of time rifts.
Catchphrasewatch: "Harriet Jones [flips ID card]-- former Prime Minister." An awful lot of "Don't, just don't," and technical explanations given at breakneck speed.
Old Skool Who: The Dalek Invasion of Earth (and the film, Daleks Invasion Earth 2150 AD-- what do you want to bet that RTD had a bet on that he could make Bernard Cribbins' involvement in a Dalek invasion canonical?) for too many reasons to cite; just watch it again already. Faction Paradox (a "Shadow Proclamation" full of weird-looking Goths? Wonder where they got that idea from). The Daleks, in reverse (human hitting on the idea of covering a Dalek's eyestick with a viscous substance, but it doesn't work here). Remembrance of the Daleks (where the Special Weapons Dalek was thought of as "the abomination" by the others). Logopolis (a planet full of pale humanoids who regulate the universe). Trial of a Time Lord, part 13 (the Earth being moved across the galaxy for some reason). Destiny of the Daleks and Revelation of the Daleks (return of Davros after he was thought dead). Battlefield *again* (a multicultural UNIT which seems to follow UN administrative systems more than the original did). Logopolis, and RTD's Virgin novel Damaged Goods (hiding something by placing it a second ahead in time). The Tenth Planet (something sending an Earth-related planet off into space, plus a faintly unhinged American general running things). The Pirate Planet (stealing a load of planets which, when properly aligned with each other, create some kind of powerful field; one of them's even named Calufrax).
Everything Else: The Hitch-Hikers' Guide to the Galaxy series (Earth animal turns out to be an alien species and flees the planet at the first sign of trouble). The Omega Man (a race of black-clad albinos with Afro hair). Minority Report via Battlestar Galactica (ship run by crazy twitching creature which occasionally has prophetic flashes). Any comedy that does a parody slo-mo-running-towards-each-other and has it end abruptly. Terminator III (teleporting blonde girls with big weaponry). The Wizard of Oz (magical device that takes you home).
I'd like to know what all the *other* ex-companions still on Earth in this time were up to while all this was going on, though. "Harriet Jones, former Prime Minister... and you must be Jo Grant, Professor Shaw, Sir Alistair, Professor Chesterton, Mike Yates, John Benton, Victoria Waterfield, Dr Sullivan..." (and, since she's really from the early 2000s, what about Zoe?)