Action Girl: Averted. Derkhan is easily the most incompetent of the entire team, and also prone to bouts of hysteria. This must have been intentional, as Mieville himself has said in interviews he's bound to deconstruct the usual tropes of fantastic fiction, and readers usually expect Xena-like badassery from a woman who admitted to be a Butch Lesbian.
Derkhan's not that useful in a fight, but she's good at sneaking around. Pretty much any time she's needed to venture out in public to fetch something for The Team, she gets it safely.
AI Is A Crap Shoot: Isaac realizes that the Construct Council has an intelligence based solely on logic and the objective. As a result, it is incapable of emotion, most importantly compassion and mercy, and therefore cannot be trusted as an ally because its alliance will end the moment it sees breaking faith as the objectively superior outcome.
Alien Sky: It is mentioned that the moon has two 'daughters' orbiting it.
Bad Ass: Yagharek and Jack Half-a-Prayer fit the bill in the more classic sense of the term, though Isaac and Derkhan's sheer bravery despite possessing no combat training definitely qualify them too.
Lemuel Pigeon is rather handy when he wants to be, though he usually prefers to flee a confrontation rather than risk the loss of his money.
Big Creepy-Crawlies: The khepri males and home-grubs. Isaac mentions the infeasibility of acquiring giant insect wings for Yagharek from an assassin beetle ("Get our arses kicked.").
Bizarre Alien Psychology: The Weaver's weird mindset is represented by its non-stop, stream-of-consciousness Word Salad monologue. Its psychology becomes a key plot point, as it's perhaps the only living sentient in New Crobuzon whose consciousness the slake-moths can't consume.
Bizarre Alien Senses: The eyeless slake-moths can smell and taste the psychic energies of sentient creatures' dreams.
Bizarre Sexual Dimorphism: The khepri. Males are non-sentient, two-foot-long, vaguely scarab-like beetles. The females, by contrast, have human-level intelligence and look like someone took a female version of the male and grafted it to an attractive female humanoid body in place of a head.
Blue and Orange Morality: Most notably the Weavers, who don't have a sense of morality so much as they have a (very, very alien, to humans) sense of beauty.
Deconstructed in regards to Yagharek's crime, which is danced around for most of the book until it's revealed in the epilogue. The action's context can't be translated between cultures at all, and ultimately Isaac is unable to pass judgement except through his own lens and frame it as what the crime is to a human. The narration touches on the dilemma this imposes on him.
Bury Your Gays: In books where being a named character and being sympathetic/a decent human being is usually a recipe for death, and the named-protagonist body count runs into the double digits, Derkhan manages to make it out mostly in one piece. Key word here being mostly.
Isaac's group hire three professional adventurers, and the two men among these are a couple. One of them has his mind eaten by a slake-moth; the other blows himself (and a number of enemies) up when Isaac tells him about this.
Chekhov's Gunman: Toro is mentioned (though not by name) before she becomes important.
Also, in the first book they mention that the Ambassador from Tesh is a vagabond by custom, and in the last book this is important as the villain and source of impending arcane doom is Spiral Jacobs, the vagabond.
Also true of Jack Half-a-Prayer within this particular book.
CI Is A Crapshoot: Constructed Intelligence in a cleaning machine and the Construct Council.
Clockpunk: The constructs, Isaac's calculating engines, and khepri "metaclockwork" devices like the stingbox.
Collector of the Strange: The Weaver collects scissors, and had previously collected chess sets. Isaac's vast collection of flying animals also qualifies.
Dangerous Forbidden Technique: Even the New Crobuzon government — y'know, those ever-so-responsible folks who brought slake-moths to the city in the first place and then sold them to a drug lord — doesn't dare risk mucking around with Torque.
Though, admittedly, only after bombing the fuck out of some rival cities using Torque bombs, trying - and failing - to cover up the horrific results with a Fantastic Nuke, and then almost being toppled by outraged public opinion.
Downer Ending: The few characters who don't die trying to save the city/world suffer terrible personal loss. The worst thing is that a fairly happy ending could easily have occurred if a few crucial moments had played out differently. They just didn't.
Down the Drain: Plagued by biological monstrosities (byproducts of waste materials from research facilities), gang members, and the odd multi-planar Giant Spider makes the sewers uniquely dangerous in a city filled with danger already. Isaac etc. are appropriately intimidated when they find themselves in the sewer system, and must rely on Lemuel to avoid most certain danger.
Most notably the slake-moths, which literally feed on people's consciousness, leaving them as utterly mindless shells. Even looking at them will destroy your consciousness. These creatures are so terrifying that when the government of New Crobuzon attempted to make a Deal with the Devil to deal with them, hell refused to get involved.
It's at least implied that there's something even more powerful that eats slake-moths in their native habitat, that keeps their numbers down.
There's also the Weaver, the creature the government turns to when the demons turn them down. It is a gigantic spider that exists between dimensions and is capable of traversing realities as we would walk down the street. Its normal speech sounds like free word association with no grammar, but it uses many methods to communicate (such as making a random newspaper article with its answer find its way to Isaac). Part of the Mayor's trouble with communicating with the Weaver is figuring out what concept or object it currently finds aesthetically pleasing. At one point it was obsessed with scissors and cutting peoples' ears off (except one guy in the room who it thought had pretty ears, so it reattached them). It seems to be purely driven by the subjective "beauty" of the tapestry of reality.
Whatever left behind the bones that became The Ribs in Bonetown is more or less outright stated to be this- even theslake-moths find being around The Ribs unsettling.
New Crobuzon has a catchall term, "Xenians," for all non-human sentient species. Note all three of the city's most important officials are humans. Even if Rescue is just a host for a Handlinger.
The dockworker strikes in the middle of the novel develops along racial lines, with humans who side with the vodyanoi being labeled as "race traitors."
The Khepri have it coming from every angle. The novel opens with Lin specifically stating that her grocer treats her well because he doesn't know she's a "bug." Furthermore, there is definitely a clash of cultures within the Khepri community; Lin even muses that she silently roots for Francine against Motley because she's Khepri, but not "good Khepri."
Fantasy Counterpart Culture: New Crobuzon is basically London, although the author has stated that other cities were also influences, notably Cairo.
Fantastic Nuke: "Colour bombs" are stated to have this effect, though exactly how they work and when they are used isn't revealed in this book (although we do learn more in Iron Council.)
For Science!: A big part of why Isaac wants to help Yagharek.
Freakiness Shame: Grimnebulin is totally hot for his girlfriend, who has a scarab for a head. He reflects at length about how his revulsion turns him on.
There are also bordellos that cater to people who want to have sex with Remade, who have had Body Horror alterations done to them. These are also technically illegal and sometimes used by the New Crobuzon government to entrap and blackmail citizens into becoming spies.
From Nobody to Nightmare: The Slake-moths are first seen as an inconspicuous parcel crossing a Parliamentary Clark's desk. Isaac hangs onto the runt for most of the early novel, where it is seen as little more than a curiosity until it hatches and eats Lublumai's mind.
Genius Bruiser: Isaac, in spite of being a scientist, holds his own against the city's militia with some well-lobbed chemicals, not to mention taking on monsters that Hell itself was too scared to fight.
Heroic BSOD: Isaac's response to finding Lin's head-wings enclosed with her ransom note. In the ending, most of the surviving protagonists are deeply shaken (Isaac, Derkhan) or broken entirely (Yagharek, Lin).
Laser-Guided Karma: Happens, in a small way, to Mr. Motley. One of the slake-moths he purchased from the government lobotomised Lin and facilitated her escape. Even if he found her again, his statue can never be finished. The epilogue describes him ranting at the incomplete statue.
Late to the Punchline: Finding out what "Prayer" in Jack Half-a-Prayer really means. One of his arms has been replaced with the claw of a giant PRAYING mantis.
Lightning Bruiser: The Slake-moths are so terrifying because they are fast, intelligent, capable of flight, incredibly resilient, and have a vast array of natural weapons, most importantly their hypnotic wings.
Logic Bomb: Isaac uses one of these as a power source for his moth-baiting crisis engine.
Mushroom Samba: Lucky Gazid hides some dreamshit in Isaac's sandwich. Isaac doesn't realise until things start going weird(er).
Never Trust a Title: The titular station is pretty tangential to the story, with only one chapter taking place there, and even then only in passing. Near the end of the book's 600-odd pages a character dramatically announces, "We have to go to Perdido Street Station," bringing the station to the forefront again, but he later reveals he only said it to trick another character and that they don't really need to go there after all.
Nice Job Breaking It, Hero: Of all the specimens that Isaac releases when declaring his research into flight having dead-ended, the single one that he elected to keep sets the plot in motion.
Nightmare Fetishist: How else to describe Isaac Grimnebulin? He's in love with a woman whose head is a giant beetle, a bird-person turning up on his doorstep asking for a new set of wings all but causes him to squee, and he is cheerfully enchanted with one particularly weird grub netted by his black-market attempts to find flight specimens. Until that grub grows up. You know when Isaac is freaked out, shit got real. He can hold a conversation, an intelligible and productive conversation, with The Weaver.
Noble Savage: Yagharek is a subversion. Played straight with the rest of his race though.
Non-Mammal Mammaries: A female garuda is specifically stated to have "ornamental" breasts incapable of lactating. Yagharek sees a female Cactacae nursing at one point, implying that her species sports these despite being sentient plants. Averted with the vodyanoi, whose gender can be fully concealed with a loincloth.
Oh, Crap: The city rulers in Perdido Street Station, on realising that the devils are scared of their problem.
One-Gender Race: The Khepri, effectively - who subvert the standard female-only race rules by being Bee People (well, beetle people) and not at all pretty.
They do have two different genders, but show extreme sexual dimorphism: the males are mindless beetles, whereas the females are sentient and are largely humanoid.
Pyrrhic Victory: Isaac has saved New Crobuzon, defeated the Slake Moths, proved his crisis engine will work (and more importantly, kept it out of the hands of the corrupt government & the Mecha-Mooks), and hardest of all, survived. On the other hand, Lin is lobotomized, Yagharek is revealed as a rapist, Isaac refuses to help Yagharek, and the Constructs are headed for destruction. Not to mention Isaac and Derkhan have to flee New Crobuzon with the lobotomized Lin in tow, as the government is understandably not interested in giving them credit for having saved the city and has left them at the top of the Most Wanted list.
Quizzical Tilt: Yagharek does this once and it looks so avian that this simple motion actually shocks Isaac.
Rape Is a Special Kind of Evil: Deconstructed. When another Garuda attempts to explain Yagharek's crime to Isaac, "rape" is the only human word she has available to describe it to him. Isaac, because of this trope, immediately leaps to all manner of (human) emotional responses and conclusions about the crime that are completely wrong from her point of view: The Garuda have noconceptof 'rape' like humans do. To them, Yagharek's crime was removing someone's choice and failing to respect her as a concrete individual instead of an abstract ("choice-theft in the second degree with utter disrespect" in their own words); the sexuality angle is completely absent. Word of God states Isaac is literally incapable of understanding her point of view.
When Derkhan is searching for human moth-bait in the hospital's terminal ward, her musings about who might be evil enough to be selected list "rapist" second, after "militia informer" (her personal nemeses) and before "child-killer" or "torturer".
Reality Warper: The Weaver, possibly. We're never told the full extent of its powers, but one person that takes a trip with it finds, on the other side, that his gun has been turned to glass.
Renaissance Man: Isaac dabbles in virtually ever science under the sun, often exploring new, underresearched areas just due to his obsession of the month. (And he manages simultaneously to not be an Omnidisciplinary Scientist; he doesn't know everything, so when someone comes to him with a new problem he has to spend weeks researching it and sometimes consults with experts in the fields he's not so good at.)
Scary Black Man: Isaac is described as having skin the color of smouldering wood, he's very fat (meaning he possesses Stout Strength, which is described below) and knows how to use his not inconsiderable bulk to intimidate (see an amusing scene where he drives off a Godmech Cog and uses his bulk for this purpose.) and has a couple disturbing interests.
Schmuck Bait: The Torque, at least to scientist-dabblers. Isaac spends some time explaining, with graphic illustrations (mostly left to the reader's imagination), exactly why messing with it is a really bad idea.
Super Toughness: As if the slake-moths weren't dangerous enough already, they also partially exist on multiple planes of existence, meaning that one must either attack them on multiple planes (which the Weaver is capable of doing, but unfortunately is too heavily outnumbered to take advantage of) or deal an extraordinary amount of damage on this one.
Take That: The book includes a good-natured jab at the typical role-playing-game adventuring party, who are looked upon by the thoroughly urban protagonists as a bunch of psychotic tomb-robbers.
Unspoken Plan Guarantee: Various people come up with plans to deal with the slake-moths, which for the most part fail miserably. Isaac's plan to merge the Construct Council's and Weaver's "thoughts" and channel them through Andrej is not revealed until it is well underway, and it works.
Voice of the Resistance: Runagate Rampant. Although it also has competitors/comrades in the form of other underground papers "The Forge" and "Shout".
What Happened to the Mouse?: After David Serachin is revealed to be a traitor, he just disappears from the book and never mentioned again.
Whip It Good: Yagharek's weapon of choice, with which he saves part of Lin during the final battle.
Word Salad: The Weaver. Also, Isaac's experience while under the influence of dreamshit.
The Worf Effect: Lemuel's bodyguard, Mr. X, is presented as an intimidating Badass through and through. Not only does a slake-moth kill him virtually instantly, but it does so simply to have something to throw at its intended target.
Xanatos Speed Chess: Isaac, by the end of the book. And he's playing against four different opponents simultaneously.