The Unquiet Dead: Christmas Dickensiana, also featuring homeless aliens trying to take over the Earth.
The Christmas Invasion: Christmas setting featuring regeneration crises, and questions about the Doctor's identity. The Doctor gets, and accepts, a dinner invitation.
Rise of the Cybermen/Age of Steel: Mrs Hartigan's "Turn left, turn right," routine is a deliberate echo of Mr Finch's playing with the converted; Cybermen chasing people through the corridors and back staircases of an old house; Cybermen hiding out in underground tunnels and snagging a local power-hungry maniac to convert into their leader.
The Runaway Bride: Christmas setting involving red/red-clothed queen who is trying to save her race from genocide; improbable physics regarding the Thames. The Doctor gets, but declines, a dinner invitation.
The Shakespeare Code: Bitchy evil feminists involved in the conjuring of portals around premodern London (and watch for a Shakespeare cameo on the London info-stamp).
Daleks in Manhattan/Enemy of the Daleks: Small band of classic DW villains are thrown into the past and, low on power, make use of local technology and workforce to try and build themselves up again; the "Cybershades" are a close analogue of the Daleks' pig-slaves. Both Dalek Sec and the Cyberking are hybrid creatures whose merging doesn't quite go according to plan, leading to an internal power struggle between them and their followers. The Doctor offers the Cybermen here the same deal he offered the Daleks before-- relocation to another planet provided they leave humanity alone.
Last of the Time Lords: The Doctor's messiah complex surfaces again.
Voyage of the Damned: The Doctor's Tarzan act on the pulley is a direct visual steal from his using the angels for flight.
The Sontaran Strategem/The Poisoned Sky: Frustrated intelligent person allies self with aliens bent on taking over the Earth, then is rather surprised when the rest of the world doesn't see their plan as anything but horrible.
Journey's End: Something that appears to be a regeneration but isn't, which leads to the creation of a human analogue to the Doctor.
The New Series Generally: Rosita has a name which is a merging of Rose and Martha, and seems to have Donna's personality to go with it. The Next Doctor is every bit as much at home in Victorian London as the current one is in modern London.
Catchphrasewatch: Between the pair of them, the Doctors get off some "Allons-y,"s, one "No no no no no," and a "Brilliant" or two, with the Cybermen wandering around muttering "delete" at intervals.
Old Skool Who: Big Finish anticipate this heavily, with "The One Doctor" featuring a fake Doctor and companion team, and "Minuet in Hell" a man who is convinced through alien influence that he is the Doctor. Doctor Who: The American Telemovie brought us a faintly-ersatz Doctor with a penchant for cod-Victoriana. Earthshock has the Cybermen searching their database for info on the Doctor's past lives, in black and white. The War Games features people with artificially altered memories. Remembrance of the Daleks (villains who gain the power of imagination by wiring a human into a computer).
Everything Else: Not only is the setting Dickensian, but there's a straight-out A Christmas Carol reference in the Doctor's conversation with the urchin at the start. Lionel Bart's Oliver! (you keep expecting the Victorian extras in the background to burst into song). Chitty Chitty Bang Bang has the cod-Victorian protagonist, and his offspring, rescuing an underworld full of dirty-faced oppressed children from the machinations of the Child Catcher, as well as some proto-steampunk chic. Little Orphan Annie featured the villainous Miss Hannigan, a power-hungry, child-hating orphanage matron with a fondness for saucy double-entendres. The Cyberking references, as well as The Iron Giant, the Japanese "mecha" genre of films and animes, featuring giant robots attacking cities (in particular, Science Ninja Team Gatchaman has a hermaphrodite villain with a fondness for siccing improbable mecha, including a giant robot mummy, a giant scorpion and a nest of giant ants, upon Tokyo). Around the World in 80 Days features balloon-related Victorian shenanigans.