Alien Sea: The Neath does not follow all of the same physical laws as the Surface, and its zee is coloured between black and green.
An Entrepreneur Is You: It might not pay so well as exploring distant kingdoms or hunting pirates, but most captains will spend at least some time ferrying goods and passengers between ports.
Ascended Meme: Ratsending. One player began using Fallen London's basic gifting system to send the lead dev thousands of rats. The mythos of transported rats expanded by degrees; a Pneumatic Ratsender is now available as a ship component.
Call a Hit Point a "Smeerp": Your ship's stats are all named for Fallen London's mysterious rulers, the Masters of the Bazaar - Iron for attacks, Mirrors for observation and illumination, Veils for speed and concealment, Hearts for healing and morale, Pages for knowledge and diplomacy.
Also, your Hull score is essentially a hit point meter; in combat it's usually what soaks up attacks, and when it hits 0 your ship sinks.
Church Militant: Abbey Rock, the coastal convent-fortress of the martial Sisterhood, and Godfall, home to the boisterous pirate-monks who follow the ways of "St Stalagmite."
City on the Water: The New Khanate's cities are variations on this style: Khan's Heart and Khan's Glory form a stately City of Canals on a series of artificial islands, while the other side of the Enemy Civil War, Khan's Shadow, is a colossal assemblage of ships roped together.
Contest Winner Cameo: A number of Kickstarter backers appear in-game as crew, secondary characters, and the names of geographical features.
Cool Boat: Several, including the trimarans of the New Khanate; the partly-organic Cladery Heart; the submarine Irrepressible, with its irrigo-cannon and breakfast-pit; and the dreaded Tree of Ages, crewed by giant spiders. Even your own ship might count, if you buy enough upgrades.
Darkness Equals Death: In a similar system to Amnesia: The Dark Descent, extinguishing your ship's lights can help you hide from enemies and creep past zee-monsters without waking them, but the darkness prevents you from navigating or seeing foes clearly and drains your crew's Sanity Meter.
Honest John's Dealership: Leadbeater & Stainrod are the Neath's largest, cheapest, least reliable provider of ships, ship components and ship repairs. It's entirely possible that they actually want you to drown.
I'm a Humanitarian: Always a risk when lost at sea, with limited supplies and a cook who's going quietly insane.
Interface Spoiler: The trading interface shows the existence of certain items and trade goods before you're likely to find them in play. Notably, the end reward of the Genial Magician's storylet is shown, even before you recruit him.
Living Ship: The Cladery Heart, a colossal, living heart, clad in iron and set to sea.
Macrogame: When a game ends, the player can begin a new game with their previous captain's maps, one of their officers, or a boost to one of their skills. Wealthy captains can also write a will, allowing their house and some of their wealth to be passed on.
Mad Artist: The Set, a group of highly eccentric and vicious artist-pirates.
The Mutiny: A ship's crew may mutiny against their captain if Terror grows too high. If they can't be talked down or beaten down, game over.
Nautical Folklore: Zailors are superstitious folk, and it's a foolhardy captain who neglects their traditions. Harming zee-bats is unlucky, stones falling from the roof are unlucky, smooth black water is unlucky, asking questions about pigs is unlucky...
Ocean Madness: It has less to do with the fact that the zee is inherently maddening and more to do with the fact that it is dark, monster-infested, and prone to rearranging itself, but Terror will be your constant sanity-draining bane.
Purely Aesthetic Gender: As is standard in Failbetter games, the Player Character can be male, female, or fit any of a number of other descriptors, without limiting their stats or even their portrait.
Real Time with Pause: Combat and zailing play out in pauseable real time. The clock stops when you have the Gazetteer open, which is usually in a port.
Resources Management Gameplay: Fuel and supplies are necessary to run the ship and maintain the crew, and their use and conservation must be balanced.
Sanity Meter: The Terror and Hunger stats track the crew's mood. An unhappy crew is at greater risk of going mad and eating each other.
Screw This, I'm Outta Here!: How you "defeat" Mt. Nomad-as the "grand-daughter of the Bazaar" (yes, that one), it's functionally immortal...but isn't immune to serious injury. At zero Health, you inflict such a bad wound that the Genius Loci decides to cut its losses and submerge to safety underneath the zee until the next Alteration. While you can loot it, it's not so much you harvesting its corpse so much as sending your crew to get as much from the sinking island as they can before it is fully underwater.
That's No Moon: Lifebergs and Mt. Nomad look like bits of island. They are not. What they are is hungry. Or just plain murderous, in the former case; it's specifically noted that lifebergs kill purely out of malice, not hunger.
Turtle Island: The Chelonate, a city built on the floating carcass of a colossal turtle. Its inhabitants subsist largely on the the products of the zee - they wear sharks' skin and drink their blood.
Volcano Lair: Mount Palmerston, the hiding-place of Hell's exiled royals.
Wooden Ships and Iron Men: The ships are iron with hearts of steam, but the vast, dangerous and largely unexplored Unterzee is a setting much more like the Age of Sail.
Wretched Hive: The Corsairís Forest, a "treacherous region of rogues and scoundrels", built on the sides of stalagmites.