First off... as before, with Gridlock, let me say that I thought this was outstanding-- but that I'm still Recyclingwatching anyway.
And, as before with the Dalek two-parter, this one's just going to be an addendum post, putting in any new recycling, or any previously-mentioned recycling that's either become a bit more obvious or acquired a twist, or otherwise become mentionworthy.
The Unquiet Dead: Plucky girl housemaid saves the day; a human being makes a conscious decision to die so that the Doctor can live.
Aliens of London/World War Three: I've said it before, but Lawrence Miles put it better in his blog: "The Doctor describes these aliens as hunters. They track their prey by smell. They have a strong sense of family. They insert themselves into human bodies, they've got a thing for strange gases, and they clearly prefer fat victims. Even Rebekah Staton looks like a younger, cuter Annette Badland. Is the message not clear, I asked myself?" Apparently RTD has said that he based the Slitheen on the Family of Blood, so this is kind of the ouroboros of recycling here.
Boom Town: Introspective conversations between the Doctor and someone else, the upshot of which is that, seen from the perspective of those who catch the fallout, the Doctor's really not such a nice guy after all, even when he's trying to be.
The Parting of the Ways: Moral decision time for the Doctor. The Doctor's cell structure changes, turning him into someone else.
The Girl in the Fireplace: Well, this one's got a girl in the mirror, but it's also got a woman who loves the Doctor but is willing to let him go because she loves him. The Doctor meet someone as a child, then fast-forward to when he's an old man.
The Impossible Planet: Mother-of-Mine getting chucked into a black hole.
Love and Monsters: Being on the fringes of one of the Doctor's adventures wrecks a whole bunch of human lives, but one of them, who's been having mysterious dream-visions, suddenly has them all make sense for him.
Old Skool Who: Battlefield (war memorial sequence; anti-war message). Any of the Cartmel Dark-Doctor stories and the NA's they spawned (emphasis on the idea that the Doctor's really a bit of a bastard, if you see it from someone else's perspective); special mention again to "The Curse of Fenric," featuring a baby, and a baddie who is trapped in a flask for all eternity; "The Five Doctors" (Borusa wants eternal life and gets it but in an ironic way); any humans-taken-over-by gaseous-aliens story you care to mention. The American Telemovie (featuring a half-human Doctor, though they may have nicked that one from Cornell's book to begin with, so it's sort of another ouroboros-recycle). Warrior's Gate (dwarf star alloy, and people living inside mirrors). The Enemy of the World (Tardis doors opening and a baddie being sucked out). The Wheel in Space (the sequence where the Family line up the schoolboys and go through them looking for the Doctor resembles the Cybermen going through the crew manifest with the same intention).
Everywhere Else: If again, in spades; Oh! What a Lovely War (ironic use of hymn music over battlefield sequences); Twelve Monkeys (thanks to Lawrence for this one); Battle Angel Alita (OK, I don't know if Paul Cornell's ever seen this, but there's a sequence fairly late on where Alita experiences an alternate world in which she didn't grow up a warrior-cyborg, but instead had a normal human-style life; and, seductive as this option is, she makes the conscious decision to end it so that she can save her friends). The Sapphire and Steel story about the man who lives in every photograph ever taken (the fate of Sister-of-mine).