Nightfall Series: In Franka’s backstory, when Prince Vladimir walks through the yard in the Tower of London to meet with the Duchess, a flock of ravens rises up and flies away. The legends say that the ravens at the Tower would only leave it once the Kingdom has fallen, which is exactly what is happening.
The works of Neal Stephenson can be read and enjoyed without advanced knowledge of computer science, meme theory, classical and ancient mythology, international finance, particle physics or the geopolitical dynamics or history; however, readers who are familiar with those topics have a massive head start when it comes to figuring out what the hell is going on.
In Julian Comstock, while Adam is assisting a doctor with amputations during the Goose Bay campaign, a soldier who is posing as a priest uses parts of a Walt Whitman poem as an impromptu prayer for the wounded. During the American Civil War, Whitman volunteered as an army nurse and did much to publicize the experiences of medical personnel and wounded.
The Michael Crichton novel Sphere involves a cryptogram. A plot point is that a character deliberately errs in solving it, changing its meaning by changing one letter. The deception is not revealed until much later in the novel, but if the reader solves the cryptogram himself, he discovers it right away.
George R.R. Martin's series A Song of Ice and Fire contains plenty of events/people drawn from European History. Many readers tend to think the world is spectacularly cruel, until you realize that many of them actually happened. Among others, there's War of the Roses, the Rape of Lucretia (if you squint), etc..
The Discworld series is plenty accessible, and damn funny even if you're not a genius, but there are hundreds of subtle jokes and references in the books that are easy to miss if you're not well versed in a number of subjects. The Terry Pratchett L-Space wiki has compiled annotations and references.
Alfred Bester's The Demolished Man features a code key of various business phrases in its first chapter. There are so many listed that readers will likely just skip over them. However, if you actually apply the key to the messages sent and received in the chapter, you'll see that the message a character claims is a rejection of a merger request is actually an approval of the merger. This becomes very important toward the end of the book.
House of Leaves is stuffed with references both to entirely fictitious and real works, mixing them up for maximum confusion. Astute readers, however, will start noticing the references to Jorge Luis Borges, author of "The House of Asterion" and "The Library of Babel"... including a multiple-paragraph quote from Pierre Menard: Author of the Quixote.
The novel also contains numerous references to philosophers like Derrida and Heidegger, who are known for their theories on language and textuality. Heidegger specifically is known for his notion of 'Unheimlichkeit', meaning both creepy (uncanny) and unhomely. Also, and according to him, "language is the house of Being."
There's comparatively easy Pynchon, and then there's stupefyingly intimidating Door Stopper Pynchon. The former would include The Crying of Lot 49, his "Whatever happened to the 1960s?" novel Vineland, a few short stories like "The Secret Integration" and his recent book, Inherent Vice. These offer a healthy dose of Genius Bonuses, while V,Gravity's Rainbow,Mason & Dixon and Against the Day head over into Viewers Are Geniuses territory.
A lot of jokes and references in John Hodgman's Complete World Knowledge series will fly over readers' heads unless they have enough historical, geological, or pop cultural knowledge to understand why they're funny.
Neil Gaiman's American Gods is, not surprisingly, rife with references to religions around the world, so much so that the forums on his official website are filled with guessing games as to the identities of many of the more obscure ones. Anyone who knows the origins of the English days of the week will know who Mr. Wednesday is as soon as he's introduced: Wednesday is named for Woden, a Germanic name for the Norse god Odin. He even drops a big hint when he mentions that today is his day (meaning that Shadow is meeting him on a Wednesday), but because of the stormy weather, it might as well be Thursday. Thursday is named for Thor, Odin's son and the Thunder god.
T.S. Eliot's poem The Waste Land contains so many obscure references to different works that it makes the reader wonder if they are reading a poem with footnotes or footnotes with a poem.
Kim Newman's Anno Dracula is filled with a massive cast of historical figures, 19th century fictional characters, and more recent vampire horror characters, all swanning around in a London where Dracula survived and married Queen Victoria. You need an encyclopedia to catch all the historical references and literary in-jokes.
The Artemis Fowl books have some fun wordplay, the notable example being in Eternity Code.
Try saying the names of the rival telecommunications companies out loud. They are "Phonetix" (think three syllables) and "Fission Chips" (perhaps less erudite, but still amusing).
Doctor F. Roy Dean Schlippe, anybody?
All of his pseudonyms. Emmesey Squire probably knows quite a lot about Einstein. Dr. C. Nial DeMencha is mentioned to be a psychologist. Sir E. Brum is named after part of the brain. The Other Wiki lists them all in his article/profile.
The Dalziel and Pascoe series of novels has any number of literary references that erudite readers can pick up on.
Ghost Story: It starts on May 9th, which was the first day of the Roman festival of Lemuralia, which was when people would banish the Lemures, vengeful angry ghosts.
Cold Days: People familiar with their mythology will recognize the names Harry uses for Mother Winter as one of the Fates and one of the Norns. The revelation that Santa is an aspect of Odin will also make a lot more sense to a reader who knows about the history of the mythological figures involved.
Also in Cold Days: That same audience of mythology buffs might find a moment of particular significance during the chase from the Wild Hunt, when a rider who turns out to be Santa Claus, and therefore Odin throws a spear at Harry which turns out to pass over him rather than striking. That particular genius bonus actually counts as foreshadowing to the informed.
Attempted, but failed, in Fool Moon. When talking about a type of super-werewolf called the loup-garou, Bob mentions that the last one was seen in Gevaudan and killed a lot of people very quickly. It's meant to be a reference to the Beast of Gévaudan, but every single detail involved is wrong, from the number of attacks to the number of deaths to the resilience of the Beast to the time the attacks took place to the duration of the attacks to etc. It's a borderline Critical Research Failure.
Dr. Seuss indulged in these now and again. One particular example is when a character is charged with having "a flugelhorn ge-busted." Flugelhorns are real instruments, even if the word does sound like a Seuss invention.
Better yet, the Flugelhorn is a German instrument with a German name. Adding "ge-" to the beginning of (some) verbs in the past tense is a feature of the German language.
In Valhalla, a character named Valfar gives Violet a tour of the ravine and its power plant, which can only be described briefly as a cavalcade of quantum physics jokes, puns and concepts.
Isaac Asimov wanted to call his short story "Flies" (in which a manufacturer of flyspray is worshiped by flies as a vengeful god) "King Lear Act IV, scene i, lines 36-37", but his editor said no-one would get the reference. (It's the "As flies to wanton boys are we to the gods..." line.)
The Lord of the Rings contains several major shout outs to Macbeth, all taken from Act IV, Scene i, when the Witches tell Macbeth their prophecies of his death. First of all, the phrase "Crack of Doom" was coined by Shakespeare in this scene. And, bordering on Take That!, the Ents' besiegement of Isengard and the Witch-King's defeat by Éowyn are references to two of the three prophecies: namely, that it will not happen until "Great Birnam Wood... shall come against him" and that "none of woman born shall harm" him. In Macbeth, the trees do come to the castle when Macduff's army uses their branches as camouflage, and Macbeth is killed by a man who was not born, but removed from his mother's womb. Tolkien thought both Prophecy Twists were huge cop-outs—as such, in Lord of the Rings, when Fangorn Forest comes against Saruman it damn well is the forest doing it, and the Witch-King who no man can kill is slain by a woman, with help from a hobbit. Denethor's Take That! to "other places of less royalty" where it takes only a few years for a steward to become king is also directed at the House of Stuart, whom Macbeth was written to flatter.
While you don't need to be familiar with ancient/medieval Middle Eastern art and Islamic theology to enjoy My Name Is Red, it doesn't hurt. On the other hand, the neophyte reader gets several college courses worth of information on the subjects, wrapped up in a fascinating set of narratives.
Lovely Assistant by Geoph Essex. The few Angels of Death whose names we learn (besides Jenny) are Caravel, Ketch, Curach, Pauzok, and Voitas. If you know boats or the right languages, the shout out to The Ferryman guiding the dead to the afterlife is a fun bonus.
Geoph Essex does this again in Jackrabbit Messiah:
If you know the etymology behind the name of Chicago, then the description of the city mentioned by a more knowledgeable character(actually Ketch from Lovely Assistant!) earlier in the book makes perfect sense. The place inside the Prince/Princess of Chicago's head is subtly described to full of wild onions, there's some play with metaphors of certain people having "layers within layers", and there's the less subtle pun in the name of the place where the heroes first find the Prince of Chicago.
And readers who understand the Hindi word Indra uses to refer to Caleb O'Connor (right after meeting him) have a little head start on Caleb's backstory, assuming Indra isn't just insulting Caleb like he does everyone else. He's not. The word ties up a Meaningful Name triple play, too, if you also know how both Caleb's first and last names are derived - it's very unlikely that Essex didn't do that deliberately.
The main character of the obscure children's book Sleepers, Wake by Paul Samuel Jacobs states that his favorite organ piece is Bach's Sleepers, Wake, an alternate name of the chorale prelude Wachet auf, ruft uns die Stimme (BWV 645). Obviously, the intended audience of the book would not know what Jacobs is talking about. Even most parents wouldn't know about the piece because of how obscure Bach's chorale preludes are to the general public.
The Genius Bonuses are practically nonstop in Catherynne M. Valente's The Orphan's Tales. Valente was a medievalist scholar, and a little research into monsters and mythology of the medieval period will reveal how many creatures she borrowed from pre-existing stories. Like African cyclops that are at war with griffins, dog-headed men, people with one giant foot, goldfish that can turn into dragons if they swim over a waterfall (Japanese myth, along with polite kappas and fox-women), even huldras. Yes, one-third girl, one-third cow, one-third tree? Authentic Germanic myth!
Simona Ahrnstedt has put a lot of research into her historical love novels. Överenskommelser has a mention of the royal wedding, that really took place in Sweden in 1881, and also name-drops celebrities like Claude Monet, Charles Darwin and Henrik Ibsen. Betvingade features three real historical personages: King Magnus, Queen Blanche and Saint Birgitta. De skandalösa name-drops Niccoló Machiavelli and Galileo Galilei and features king Carl XI.
Two alien races in The Osmerian Conflict the titular Osmerians and the Silicians are primarily made of Osmium and Silicon respectively. Their physical appearance and chemical make up reflect this and are used as defining traits.
The Man Who Brought The Dodgers Back To Brooklyn is chock full of these for fans of baseball history. One prominent example is that, in this universe, a team called the LA Stars is incorporated as a National League replacement for the departing Dodgers. In reality, there was a Pacific Coast League team called the Hollywood Stars who were one of two teams displaced from LA when the Dodgers moved to the city in 1958. Even better: the PCL was on the cusp of becoming the third major league before the Dodgers moved, meaning that the Real Life Stars would have been one of LA's major league teams if not for the Dodgers.
In Murder at Colefax Manor, those familiar with classical music will recognize that sheet music on Lord Colefax's piano relate to death, punishment from a god, and a sea cave, the latter of which is an important location towards the end of the book. The door signs in the caverns and Legrys Mor's name are both untranslated Cornish.