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.
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.
Badass Bookworm: 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.
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.
Bury Your Gays: Oddly averted. 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.
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.
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.
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.
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.
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.
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.
Averted in that the "victim" explicitly doesn't accept that label or consider herself damaged. Played straight (or doubly averted) by how the protagonist reacts- Word of God states he was literally incapable of understanding her point of view.
The circumstances are rather special here: according to the garuda's Blue and Orange Morality, it was less the rape than Yagharek's removal of his victim's choice not to have sex with him that the garuda find unacceptable. They literally refer to it as choice-theft in the second degree. The first degree being murder.
The bulk of the plot stems from Yag's quest to escape the consequences of his deed. The fact that he fails, and even mutilates himself further, may indicate that this trope is actually being played straight.
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".
Renaissance Man: Isaac dabbles in virtually ever science under the sun, often exploring new, underresearched areas just due to his obsession of the month.
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.
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.