Gene Wolfe's masterpiece set After the End in a Feudal Future which seems to be Low Fantasy, but is actually science fiction - though this is only subtext during the first four books, becoming overt in the coda. It tells the story of Severian, an apprentice of the Torturer's Guild who turns out to be a kind of Messianic Archetype.The tetralogy consists of The Shadow of the Torturer, The Claw of the Conciliator, The Sword of the Lictor and The Citadel of the Autarch, plus a coda, The Urth of the New Sun, which was written some time later and clears up a number of points from the series proper. It's a work of staggering complexity, with very little explained outright. The Wild Mass Guessing alone would be longer than most pages on this wiki (and here's proof).Part of the "Briah" Cycle, along with the Book of the Long Sun tetralogy and Book of the Short Sun trilogy.
Also our hero, who is a trained torturer and executioner, and often defends those occupations as necessary parts of society.
Though one of his first acts as Autarch is to lock up the members of his guild in the oubliette for a while to see how they like it, and then to issue an order banning torture and dissolving the guild. "By our mercy we will grant even the foulest a quick death. Not because we pity them, but because it is intolerable that good men should spend a lifetime dispensing pain."
All There in the Manual - The rare supplementary books Lexicon Urthus by Michael Andre-Driussi (which explains some of the more oblique aspects of The Book of the New Sun, as well as the archaic terminology) and The Castle of the Otter (a collection of essays by Wolfe himself about various aspects of the series).
Also GURPS New Sun, the RPG, which includes a lot of background hints.
"Attending Daedalus: Gene Wolfe, Artifice and the Reader" concentrates on the techniques used by Wolfe to guide and misdirect the reader.
Animated Armor: Sidero in Urth of the New Sun. He is not happy when Severian wears him.
Artificial Human: Jonas. Also, Dr. Talos turns out to be Baldanders' homunculus. Master Malrubius in his post-death appearances is this as well.
Back from the Dead: Dorcas and several others, including Severian himself, in all probability thanks to the Claw of the Conciliator. Also Dr. Talos, if we're to assume, as it's implied, that Severian hit him a little too hard and broke his neck during their previous meeting.
Banana Republic: If you believe that the story is set in future-South America, then the massive inequalities of its feudal system is just a futuristic spin on this trope.
Word of God says Urth is not, in fact, Earth in the distant future, but takes place in another iteration of the universe.
Big Labyrinthine Building: The House Absolute. Not only is the House so vast and complex that its extents are unknown, but there is a secret "Second House" coextensive with the first.
Body Horror: Baldanders has attained eternal life at the cost of ceaseless growth. The implication is that he's become a humanoid cancer.
Brain Bleach: In Baldanders castle/laboratory, Severian runs through a room whose central feature is a wide-awake vivisected pregnant woman under glass. Spoilered not because you don't know Baldanders is evil, but because it's so disturbing.
Also,Severian bumps into a gigantic infant (that is, the size of a full-grown man) chained to Baldanders's bed. Even Severian is sharp enough to think "catamite."
Also, at one point it becomes necessary for Severian to crack a man's head open and eat his forebrain while he's still living. Yeah.
Brother-Sister Incest: Agia and Agilus. Possibly inter alia, if Severian's missing sister, Severa, is Jolenta or Juturna.
Call a Smeerp a "Rabbit": As if inverting the popular fantasy trope is not enough, Wolfe subverts it for good measure by naming most of his alien, genetically-engineered or otherwise exotic creatures after obscure prehistoric beasts. Apparently not one term in the tetralogy was made up by the author.
That claim has confused quite a few readers due to unfortunate typos such as "onegars", a type of animal no one could identify. Turns out it's a typo for "onagers"; onagers are donkey-like animals. (Wolfe gave the definitions for a lot of the weirder words in his book "The Castle of the Otter", which is well worth reading.)
Christianity Is Catholic: Wolfe is Catholic and the religions existing in the world are based upon Catholicism. Justified perhaps by the Epileptic Trees theory that the novels are set in future South America.
Covers Always Lie: The back cover of the compilation version of The Sword of the Lictor / The Citadel of the Autarch describes the book as containing "Severian's final showdown with the evil Autarch." Not only does this never happen, but to top it off, the "evil Autarch" is an affable eunuch with a penchant for flamboyant attire. No, not Affably Evil. Just affable.
Cold-Blooded Torture: The Torturer's Guild tortures people as punishment, not interrogation and has no interest in the innocence, guilt, or any attributes of their victims.
Crystal Dragon Jesus: In a very Future Imperfect way, religious orders exist that are remnants of Christianity but have become really odd. The Torturer's Guild seems to be a warped version of the Catholic priesthood, as they still think about Saint Catherine in terms of a patron saint and torture is thought of as a messed up version of Confession. Even their formal name, "The Order for the Seekers of Truth and Penitence" equally describes torturers and Catholic clergy. There are the Pelerines who are like nuns but with some Eastern religion thrown in. Finally, there is the ritual of the Alzabo wherein you can gain someone's memories by eating their body along with this alien creature, which has echoes of the Eucharist.
It goes even further than this. There is an actual Crystal Dragon Jesus in the form of the Conciliator. The religious orders are not actually remnants of Christianity but parallel to Christianity; angels, prophets and healing powers are all very much real. Christianity doesn't exist yet because the New Sun's universe is before our own.
Sort of. The New Sun's universe is cyclic, so Christianity may have existed, but not in the same form as in our (later) universe.
And the Conciliator, though being set up to be a distant memory of Jesus, is really Severian himself, via time-travel.
Chillingly subverted in that the Conciliator myth is engineered by Sufficiently Advanced Aliens to make it appear that their plan to destroy/renew Urth has a divine purpose. Arguably the entire plot is about Severian being manipulated into believing he is on a divine mission, so that he will create the Conciliator myth.
Cue the Sun: An apparent miracle attibuted to Apu-Punchau.
Dead All Along: Severian. For clarification, in the coda, Urth of the New Sun, Severian died early in the book but immediately had all his memories implanted into a new, identical body that Tzadkiel fashioned for him on the spot.
Unless he died earlier than that. And there's reason to think he did... there's a skull at the bottom of the river where he "nearly" dies in the first book.
Deadly Euphemism: The Torturer's Guild refers to its victims as "clients"; also, its technical name is "Guild of The Seekers for Truth and Penitence."
Deus ex Machina: in book four when Severian is rescued by aliens in a spaceship (who had been introduced earlier). His rescuers explicitly state that they are pulling a Deus Ex Machina. However, it is likely that this is a subversion rather than simply lampshading an unsatisfying plot development: the thoughtful reader is supposed to connect this with the puppet imagery earlier in the narrative, and wonder what else the 'powers from above the stage' have been doing during the story.
Diamonds in the Buff: Jolenta's outfit in Dr. Talos' play. (Severian and Dorcas are completely naked.)
Dramatically Missing The Point: when Severian discovers a bush covered in Claws on a beach in book IV, does he join the dots and recall that aliens just told him to his face that they were "powers from above stage" orchestrating the story of his life, taking him to the beach so he would have a necessary little adventure? No. He has a religious epiphany instead.
Expy: Severian has aspects of the Emperor Claudius as seen in I, Claudius. He refers to people calling him "Severian the Mad" as well as "Severian the Lame" and like Claudius has a less than happy marriage to a woman named Valeria.
In The Urth of the New Sun he mentioned that his friends called him "Severian the Lame" and his soldiers called him "Severian the Great." This may be a shout-out to the Asian warlord Timur, who was also known by both titles. (It was apparently a pun in Timur's language.)
Also, sort of a combination of Expy and Shout-Out is the Librarian Ultan who Severian meets, who is clearly based on the author Borges.
Which in turn suggests Borge's story Funes the Memorious, about a young man with a voluminous memory, who is so weighed down with details that he is incapable making the generalisations needed to truly understand those facts - which shows us how Severian is an Unreliable Narrator.
Abaia is arguably an Expy of Cthulhu.
Five-Man Band - subverted to hell and back with Dr Talos' players, who Severian crosses paths with and then leaves, several times. Severian even meets Dr Talos and Baldanders in an inn.
Future Imperfect: Several examples. While at the library, Severian sees a picture of the first men on the moon and not only describes it in an Innocent Inaccurate way, but also wonders why there's no vegetation on it. Another scene makes reference to the planet Mars being renamed "Present" at some point and one character can't believe a language existed where the words for "gift" and "now" were the same. There's also a scene where Severian hears a story which has a definite similarity to that of Theseus, but has no idea of the connection. Long lived robot Jonas does understand the connection though.
Actually the story is a mashup between Theseus and the Battle of Hampton Roads: the joke is that after so many centuries, people got the Minotaur confused with the Monitor. (There's a similar story that is a mashup of The Jungle Book and Romulus the founder of Rome - both children raised by wolves.)
The further joke being that the unnamed hero is dreamed up by a student - confusing 'Theseus' with a thesis.
The ship being called The Land of the Virgins is intended as another pun. It ties in nicely with the sacrifice of maidens to the Minotaur, but the joke is lost anyone who isn't from the South and therefore thinks the name of the ship that fought the Monitor was the Merrimack, not the Virginia.
Genetic Memory - Severian, after ingesting alzabo gland extract and eating part of Thecla, inherits her memories.
Note that while he's a giant already, he's not even close to full-grown. He will get big enough to have to live in the water eventually, among the Undines and other giant-types too big to walk on land, which as the comment above states, seem to have eerie abilities - there's a throwaway reference to them swimming between the stars.
God Guise: Tzadkiel appears to Severian in the form of an angel. He falls for it.
Torturers are forbidden to marry (because their wives would be outcasts the same way torturers are, but without the compensations of belonging to a guild and knowing they are a critical part of the government apparat.) However, they aren't required to be celibate, and they seem to hire prostitutes whenever they can scrape the money together; also, they're occasionally required to sexually assault the prisoners as part of a court-ordered punishment. Severian's behavior towards women is surprisingly considerate for someone who spent his entire childhood in this environment. (As he says at one point, he's a bad man trying to be a good one.)
Homage: Many of the shorter stories encountered throughout the main text contain more or less obvious parallels to real-life mythology and literature. One is quite clearly the first chapter of Rudyard Kipling's The Jungle Book, mashed up with the myth of Romulus and Remus and an American Thanksgiving story.
Compare and contrast the Man-Apes in the mines with the Morlocks from The Time Machine (which also features the dying sun).
Have We Met Yet? - Played straight and inverted at the same time. The Hierodules are constantly moving backwards in time, while Severian moves through time normally - hence, his last meeting with them in Urth of the New Sun is their first meeting with him.
Improbable Weapon User - Severian and Agilus, during their duel, use plants whose poisonous leaves are picked and thrown like darts.
Incest Is Relative - Dorcas is Severian's grandmother, although neither of them know that at the time. Agia and Agilus are brother/sister lovers and may also be related to Severian, who has a definite thing for Agia.
Informed Attractiveness - As with other aspects of the books' world, standards of beauty appear to undergo a ton of translation loss between actuality and the narration. There's a strong chance that many of the books' most "beautiful" characters would appear downright unsettling to our eyes.
Consider the unnatural height and alien-influenced appearance of exultants, whose numbers include Thecla, Vodalus, and Thea. The exact degree of their distinctive height and features is vague, leaving it uncertain whether they'd strike us as beautiful people or as borderline HumanoidAbominations.
Innocent Inaccurate: Severian combines this with being a straight Unreliable Narrator. He's more of the former in describing the world he lives in (e.g. his description of a photo of the moon landing), but is more like the latter in describing his own life.
Maybe not just the United States. The Ascians are north of the equator, and apparently not part of the same continent as the Commonwealth, but that could include Mexico and Central America as well. (Considering how cold Severian's area is, much of the US is probably too frigid to live in.) Note that the word "Ascian" is derived from Greek and means 'without a shadow'; it's an extremely archaic term for inhabitants of the tropics (where the sun is directly overhead at noon twice a year, thus the only place where a person can stand in full direct sunlight and cast no shadow). The idea is that the common people realize the Ascians are coming from the north, but believe them to come from northern South America near the Equator rather than an entirely different continent.
However, Wolfe himself has pointed out that one-to-one matchups of places is largely not going to work, as the novels are set so far in the future that the sun is turning red, and continental drift would make places unrecognizable.
This is arguably an example of misdirection on Wolfe's part because the sun is dying prematurely thanks to a "black worm" placed at its centre - the novels may take place "only" a few thousands or millions of years in the future, before the continents have been significantly reconfigured.
Invoked Trope: The messiah, in the form of the Conciliator, is engineered by 'powers from above the stage'.
Kavorka Man: Severian is ugly, often misogynistic, and, you know, a professional torturer and executioner - but the number of women who don't seem to mind is rather staggering.
Maybe. Of all the things Severian might not be accurate about, his own appearance is high on the list, as frequently occurs in real life. Also, since nobody among the common people seem to have ever heard of the Torturer's Guild, as far as they're concerned he's just a wandering headsman; not really a savory occupation, but still, a professional one and an arm of the law.
Plus, because he's such an Unreliable Narrator, he might have lied about every single sexual encounter he has in the entire series.
... which is a popular fan theory. The idea is that in Urth, male sexual promiscuity incredibly rampant. In order to establish himself as a badass Severian lied about most (if not all) his sexual encounters (which vary wildly in depiction.)
Lampshaded Double Entendre: Only sometimes sexual in this case, but Jonas' catchphrase is making "as the actress said to the bishop" type comments.
Mechanical Evolution - In The Urth of the New Sun, the mechanical humanoid Sidero is revealed to be a robot evolved out of spacesuits with built-in artificial intelligence.
Mind Screw: And how! Is Severian god? Is the whole thing a complicated twisting plot through multiple timelines? Can we believe a quarter of what Severian is telling us? And many many others. Let's put it this way, there's enough Mind Screw in here to make Evangelion look like an episode of Sesame Street.
Ironically, Severian writes that the purpose of his book is to avoid speculation about the events of his life. One can imagine Wolfe having tongue firmly in cheek when he wrote that.
Ms. Fanservice - Jolenta is a deconstruction. Her carefully (and sometimes painfully) maintained figure is a source of inconvenience, and people hate her for being so attractive even as they lust after her. Jonas is the only one who truly and unconditionally loves her for herself.
Scavenger World: Gene Wolfe once described Urth as "the future where we sit at home and wait for the money to run out" - humanity has exhausted all the resources of the planet and can no longer support any level of technology higher than medieval. Only the ruling class have access to higher levels of tech, which they get by trading for it with extra-terrestrials. In The Claw of the Conciliator Severian runs into a village of "miners" who basically make a living by robbing graves.
Show Within a Show: Dr. Talos' play "Eschatology and Genesis," which is an allegory for the overarching plot of the series.
Space Is an Ocean: Not only are sailing metaphors used for space travelers, their crafts are actually made a lot like traditional sail boats.
It goes even further. Not only are ordinary sailors sometimes employed on starships, but thanks to the difficulty of travel, other planets may as well be other continents as far as most people are concerned.
So Beautiful, It's a Curse: Subverted by Jolenta - she herself enjoys being so beautiful that Even the Girls Want Her. However, the process used by Dr. Talos to make her beautiful has left her effectively crippled and dependent on various lotions and chemicals only he can provide, without which it breaks down. Horribly.
Torture Technician: The Torturer's Guild in which Severian is raised and apprenticed. As there are, by decree, no female torturers, the guild raises such male infants as fall into their hands.
Unreliable Narrator - Severian is one of the big ones, and it is sometimes lampshaded. He claims on several occasions to have an eidetic memory - but it's quite clear that he sometimes lies outright. He also omits details that he apparently considers unimportant (or has difficulty understanding) - this extends to major events that change the course of the story.
Further, Severian's verbose (and usually (significantly) inconclusive) philosophical ramblings tend to disguise the fact that he isn't smart enough to work out what's really going on. It is an alleged trait of some real-life mnemonists - shared by Severian - that they are passive acceptors, and combine a wealth of thought with surprisingly little intellect.
Wolfe's Shout-Out to the author Borges (the libary/Ultan the Librarian) is likely a pointer to Borge's 'Funes the Memorious' as a indicator of why Severian is unreliable; Funes is a young man who's head is so full of facts that he 'can't think any more', and is incapable of making the generalisations that Severian needs to join the dots.
One reader went carefully through the novels and noticed that every single time Severian mentions his "eidetic" memory he goes on to recall something that's already happened in the novel... and gets some detail wrong. Either he's lying constantly or his memory is nothing like as good as he thinks it is. (Formatting on the link is pretty ugly; scroll down a page or so to get the content.)
Viewers Are Geniuses: They have to be to understand all of the complex etymologies, etc. used by Wolfe
Voice Changeling: The alzabo can perfectly imitate the voice of anyone that it has eaten. It naturally uses this to lure its victims family members out of hiding.
Weird Trade Union: Besides the Torturers, there are several other guilds such as Librarians and Animal trainers, as well as one of Witches, although rather than being magical, they appear more akin to a spy network.