Roots: Das Kapital and the Communist manifesto ("you have nothing to lose but your chains!" is a reasonable translation given its popular use), Jacob's Ladder (Spiridon being, as Alan Barnes suggests, the Thals' Vietnam) T-Rex's Children of the Revolution. Charley quotes Paddington Bear ("Darkest Peru"). See Enemy of the Daleks for possible origins of the substance plasteen Richard Semon's 'engram' theories.
Intertextuality: Levels of the Dalek facility 'Zeg 1' and 'Yarvell 6' take their names from TV Action comic's Daleks strip, after one-time Dalek Emperor-pretender Zeg and creator of the comic Daleks Yarvelling. Earth, the 'lost planet' comes from the Dalek Annual, as well as the continent 'Davius', presumably the origin of the name for the new Thal world, New Davius.
Charley's term 'Thaleks' is first used in the [unconnected] Unbound story Auld Mortality by Mark Platt.
Dialogue Triumphs: 'I'm not talking to the trees, I'm talking to the invisible people'
"Aren't you supposed to be dead?" "-I'm getting really sick of this!"
"You never change, will you? You Daleks... everything in the Universe changes - people learn, develop; even me - but not you. You've stagnated yourselves in evil. If it wasn't so terrifying it would be pathetic!"
Continuity: Spiridon is in the ninth system of a far-off galaxy Spiridonian flora includes the sponge plant which spreads its spores through its own sap, and a carnivorous plant large enough to attack and devour a human (the former is a suggestion by the Doctor, the latter is imagined by Charley?)
The Daleks plan to use kyropites to transmit Dalek thought processes into captive brains so they can enslave an entire species, seeding entire worlds with their ideas even before their saucers land. Dalek technology here includes clones and replicants, while the facility is powered by anti-matter reactors. The Black Dalek's awareness of Folkestone (see: Links) implies that this is in the future of Terror Firma, unless it or the Daleks travelled back from that time.
The Thals are aware of Das Capital through Murgat and have based their ideology on it. Skaro still exists in this time, although it is implied that the Thals have left this world and colonized a new planet which they call New Davius (see: Intertextuality.) Thals regard the name 'Earth' as something from one of their fairy stories, like the words 'mutos' and 'Doctor of TARDIS.' The Mechanoid wars were a previous conflict in which the Thals also fought (Valion is a veteran.)
The TARDIS measures temperature in Fahrenheit
Charley reacts to the name 'Skaro' (this is noticed by the Doctor.) She and the Doctor haven't yet discussed the concept of the Web of Time yet - at least, not in this incarnation. Charley inadvertently makes a reference to the Doctor having met Sigmund Freud and, when he denies it, she realises it hasn't happened to him yet (see: Links. Possibly this information isn't known to the replicant, but we may as well assume the replicant does know)
The Doctor says he hasn't been near Antares in six millennia.
Untelevised Adventures: The Doctor visited Folkestone on October 1914 where he met Jessica Borthwick whilst she was taking Belgian refugees in her yacht across the Channel while under fire from the Germans. He also claims to have met Arctic explorers Matthew Henson and Robert Peary, borrowing some of their Inuit garments, although it is not confirmed he did this while they were in an expedition (these combined with Mallory's gloves borrowed by the Fifth Doctor make him woefully prepared for cold weather, and something of a kleptomaniac)
Links: Planet of the Daleks, The Daleks (Temmosus, Ganatus, Dyoni are invoked as Thal heroes or gods), Charley mentions the anti-hallucinogenic properties of rosemary in The Doomwood Curse, The Mind's Eye (the kyropites and jekylls), Genesis of the Daleks ("Mutos"), The Chase ("Mechanoids"), Terror Firma. The Doctor mentions Krynoids (The Seeds of Doom) Dalek replicants (The Chase, Resurrection of the Daleks) and assumes the identity of a botanist called 'Brown' (presumably Peri). Charley recalls her meeting the Doctor on the R101 (Storm Warning) and the Daleks (Time of the Daleks) and Davros (Terror Firma) A meeting between a post-Sixth Doctor and Sigmund Freud is referenced in both Doctor Who and The Girl Who Never Was.
Q.v. 'The Web of Time'
Location: A ice planetoid on the fringe of the Antares system' during the Dalek Wars' (according to the story blurb) and located four galaxies away from Y45 (The Mind's Eye.)
The Bottom Line: "Though cowards shirk and traitors sneer, the Dalek flag is flying here!"
A dream world of fake Spiridons, Thal plots that are actually Dalek plots, ersatz Doctors and Charleys, crib-notes Communism and pretend cleverness. Most of Alan Barnes' stories have a pretty decent idea at the heart of them; the trouble with Brotherhood is that it tries to have at least three, then buries them in several strata of false endings and teaser scenes that go nowhere, Charley's 'confession' being a well-noted example. As Spinal Tap say, there's a thin line between clever and stupid