Right, that's out of the way, now on to the Recyclingwatch.
Rose: Major landmark forms part of villains' plans; see also Rise of the Cybermen, The Idiot's Lantern; Aliens of London, Army of Ghosts etc. etc.
Aliens of London: Pig-people; the Doctor approaching a frightened pig-person in a friendly way only to wind up in a chase sequence; major world capital is invaded by aliens.
Dalek: American in black suit who has a Dalek-related secret; Daleks in the lifts; Dalek-human hybridising; "you would make a good Dalek" or similar line. Exposed Dalek mutants left, right and centre.
The Empty Child: Mid-century setting; people going to musical show to forget their troubles; bisexual humour ("You can kiss me later; you can too if you want, Frank"); the Doctor forms alliance with a group of homeless people.
Bad Wolf: Tallulah with 3 Ls and an H, meet Lynda with a Y.
The Parting of the Ways: Daleks using humans to supplement their ranks, and having moral qualms about this; Daleks backing off; American rallies a group of reluctant supporters into an impromptu anti-Dalek army.
Rise of the Cybermen: Doctor and companion land somewhere, and companion finds a convenient newspaper giving the exact date (following which they both look up to see a) zeppelins or b) the Statue of Liberty). Villains are kidnapping homeless people and converting them into hybrid things. No zeppelins, though, which is a bit surprising considering that one might reasonably expect to see one in 1930s New York.
The Age of Steel: The Doctor/companion join a queue of potential conversion victims in order to infiltrate the facility; the chief villain gets himself converted. Things in the sewers.
The Idiot's Lantern: The Doctor tampering with mid-20th-century technology to turn it into something more sophisticated; since the Empire State Building mast was actually a radio transmitter, there's a parallel between the goings-on there in "Daleks in Manhattan" and the Ally-Pally focused activities in this script. The Doctor was trying to get to New York in the earlier story (is it just me or is the RTD administration obsessed with New York? Two New New York stories, The Idiot's Lantern, and now this...), and finally makes it here.
Doomsday: The cult of Skaro get another outing, with backstory restated. Scene of Daleks backing off, and of Daleks viewing what another Dalek is seeing through its eyestick. Companion bossily confronts a Dalek about its plans.
Torchwood: Pig-people in boiler suits = Weevils in boiler suits; apparently the Torchwood website makes a bit of a joke of this, claiming that there was a suspected Weevil infestation in New York in the 1930s.
Timelash Moment: Human/monster hybrids wandering around subterranean tunnels; one of them is a hybrid of the chief villain.
The Fifth Element: Bronzy art deco sort of look; interrupted musical performance by a diva.
Old Skool Who: Where do I even begin? "The Chase" (Daleks on the Empire State Building, and it was fun to watch RTD pretend that was completely Helen Raynor's idea during Confidential); "City of Death" (compare and contrast: Sec Hybrid with Skaroth; end of episode 1 cliffhanger involving one-eyed squid creature in suit reveal); "The Dalek Invasion of Earth" (Daleks applying intelligence tests to kidnapped humans to test their suitability as slave-workers and converting them, plus the Doctor and companion joining a queue of same); "Genesis of the Daleks" (discussions of Dalek survival and racial purity, plus a kind of Dalek/human hybrid figure); "Attack of the Cybermen" (many of the sewer scenes are plagiarised from this one, particularly the one in which a shadowy figure is glimpsed down a sewer tunnel but the glimpsee doesn't discover what it is until too late; Frank being pulled off the ladder by the pig-people is also damn close to the scene where Lytton is pulled off a ladder by Cybermen; Lazlo, like Lytton at the end of the story, is a half-complete hybrid); "The Invasion" (Tobias Vaughn undergoes a partial cyber-conversion; sewer chase scenes, and again someone getting grabbed by Cybermen while trying to climb out of a sewer); "The Talons of Weng Chiang" (pig people; music-hall shows with sewers in the basement and something nasty going on involving people disappearing; something nasty and genetically modified in the sewer); "Tomb of the Cybermen" (compare the Cyberman Controller's emergence in the 1960s story with the Sec Hybrid's emergence from the Dalek casing in this one); "The Happiness Patrol" again (piggish-people in the sewer pipes; unhappy people pretending to be happy; companion makes an unplanned appearance in a variety show; how many times are they going to reference this one?); "The Five Doctors" (Phil Collinson admits on the podcast that the image of a Dalek shadow being cast on a wall before the Dalek itself is visible was taken from this one); "Revelation of the Daleks" (Dalek remnant making use of humans to supplement their army); "Destiny of the Daleks" (the Doctor discovering a Kaled mutant out of its casing and making an important mental link as a result); "Day of the Daleks" (Daleks in dark tunnels); "Death to the Daleks" (two humans up a tower on a windy night); any story involving a Dalek mutant/embryo ("The Power of the Daleks," "Resurrection," "Master Plan," etc.); and, most especially, "Evil of the Daleks" (Daleks in a past era of human history who co-opt a local ambitious businessman to fulfil their schemes, and later turn him into a kind of Dalekised human).
Everything Else: "The Phantom of the Opera" (deformed creature that lives in the sewers but is obsessed with a performer in a local show, leaves her roses and creeps up to the wings to watch her perform; the scene where Lazlo is discovered cries out for a chorus of "He's there! The phantom of the opera!" from the showgirls); any movie in which the protagonists come to New York to start a better life (likewise, the shots of the Statue of Liberty were crying out for Barbra Streisand standing on the deck of a boat singing the final chorus from Yentl); Damon Runyon (Tallulah is the pound-shop version of Sweet Adelaide from Guys and Dolls); Philip George Chadwick (1930s writer who predicted the creation of artificial biological life; cf. the Doctor's examination of the green thing from the sewers); Bugsy Malone (New York Prohibition-era goings-on; blonde showgirl named Tallulah).