Older Than Feudalism: The Aeneid (written by Virgil for Caesar Augustus) contained a shout-out to Augustus's recently deceased nephew, where Aeneas is in the underworld and sees a man with a dark cloud around him. His guide goes on with a mournful speech about how Aeneas should weep for the tragic fate of his distant descendant and describes Marcellus's tomb on the Tiber.
There's a nice shout out to The Dresden Files in the opening chapter of Benedict Jacka's Fated. "I've even heard of some guy in Chicago who advertises in the phone book under 'Wizard', though that's probably an urban legend."
The main character of American Psycho is named Patrick Bateman; a poke at Norman Bates, the antagonist of Psycho.
More Tolkien references include Ax's middle name, Esgarrouth, derived from the Middle-Earth town of Esgaroth. In The Unknown, the air force base personnel use the cover identity "Gondor Industries" on their night out at The Gardens.
Also many, many more subtle and insignificant ones, such as the six dolphins named after the main characters of Friends in book #4.
Generally, Applegate references her favorite things often in the series: Star Trek, the Rolling Stones, the Ford Mustang, Dr. Pepper, et cetera.
In The Solution, Rachel has a dream in which she morphs elephant in a crowded mall. She crushes a kid in an orange jacket, prompting someone to say, "Oh, my God! She killed Kenny!"
In A Storm of Swords Jamie, somewhat jarringly, paraphrases Robert Frost: "We have promises to keep, and long leagues before us." Naturally the line comes immediately after them being warned about how dark and deep the woods are.
In A Dance with Dragons the Windblown are discussing the Yunkai'i soldier slaves and mention how they would collapse if someone "farted in their general direction".
In Aunt Dimity and the Deep Blue Sea, Peter Harris, son of Lori's neighbour Derek disguises himself as a dark haired young man with glasses named "Harry Peters" to avoid hordes of reporters after his grandfather wrote a letter to The Times bragging about him. Hmm, a dark haired young man with glasses plagued by fame...
The first book of The Bartimaeus Trilogy has Twoflower from Discworld make a subtle and brief cameo in a marketplace for magical items containing demons (Twoflower's camera, or "iconograph", is powered by a tiny demon painting pictures really fast).
The second book features two policemen who ask Bartimaeus and his master for their identification. Bartimaeus puts a 'glaze' on the two policemen. They then forget the object of their inquiry and move along.
One of Orbis's countries is known as Tinaria. The author's wife's name is Tina. Coincidence! I think not!
The short story "The Black Sheep of Vaerlosi" by Desmond Warzel makes reference to a mineral whose unrefined form is too sharp to handle safely. The mineral is called "costnerite"—because it's untouchable.
A very subtle Shout-Out exists in David Gerrold's Blood and Fire. While one group of characters is preparing to engage on a dangerous mission, the captain tells them "Let's be careful out there." The protagonist mentally notes that it was a watchword on her previous ship, the Michael Conrad. A shout out to Hill Street Blues and the actor who spoke the line.
In The Brothers Karamazov, Fyodor Dostoevsky has several characters quote passages of The Robbers, a play by Friedrich Schiller. There are also a lot of shout outs to the works of M. E. Saltykov-Shchedrin, Alexander Pushkin, and Voltaire. Naturally, given the book's religious themes, The Bible is quoted very often.
Eric Flint wrote the novella "Carthago Delenda Est" as a sequel to David Drake's Ranks of Bronze, but the space battle scene invokes Uchuu Senkan Yamato:
Again, there was an exotic combination of old and new technology. The three great turrets of the ancient battleship swiveled, just as if it were still sailing the Pacific. But the guidance mechanisms were state-of-the-art Doge technology. And the incredible laser beams which pulsed out of each turret's three retrofitted barrels were something new to the galaxy.... Only a ship as enormous as the old Missouri could use these lasers. It took an immense hull capacity to hold the magnetic fusion bottles.
In John DeChancie's Castle Murders, one of Those Two Guys, Peter Thaxton, solves a magical murder mystery among the castle nobles. In appreciation, the king of the castle grants him a title, which entitles him to be known as Lord Peter.
The Roman poet Catullus used the name "Lesbia" as a pseudonym for the illicit lover much of his poetry describes, a clear reference to the Isle of Lesbos, home to the Greek poet Sappho, who may well have been the Trope Maker or Trope Codifier for many of the Romantic love tropes Catullus (and for that matter, much of the Western World) used in his poetry (When he wasn't being Incredibly Explicit, that is, and even sometimes when he was).
The SM Stirling novel Conquistador features South African villains with the same names as the South African antagonists of the Harry Turtledove novel Guns of the South. There is also a reference to a landholder named Morrison, like the titular hero of H. Beam Piper's Lord Kalvin of Otherwhen. Morrison's House motto is "Death to Styphon!," a reference to the "Gunpowder God" cult of the Kalvin stories.
In P. D. James's Death of an Expert Witness, there are several subtle references to the much earlier detective novels of Dorothy L Sayers, the most prominent being a discussion of whether a man struck on the head could have regained consciousness and locked himself into a building before dying, as in Busman's Honeymoon, and a character's saying "I'd rather make love with the public hangman", as in Murder Must Advertise.
Death to the French: In Sharpe's Escape (2004), one of Bernard Cornwell's Richard Sharpe novels (which were partly inspired by Death to the French), a rifleman named Matthew Dodd is separated from Sharpe's company in a skirmish during the Peninsular Campaign in 1810. Word of God is that Cornwell has acknowledged on his Web site that this character is intended to be the same man depicted by Forester in Death to the French.
Terry Pratchett loves these. For example, in The Fifth Elephant, Vimes encounters Three Sisters who are straight out of a Chekhov play of the same name. One of them want to tear down their Cherry Orchard (another famous Chekhov play). They give him the gloomy and purposeless trousers of Uncle Vanya (yet a third famous Chekhov play — and "gloomy and purposeless" tends to be Chekhov's style).
Discworld has the Ramtop mountain range, named after the system variable RAMTOP from the Sinclair ZX Spectrum computer.
In Hogfather, the conversation between HEX and The Bursar is very reminiscent of the various 'chat bots' found all over the internet.
More specifically, it resembles the mindlessly-chatty "ELIZA" program, which predates the internet by a few years.
Witches Abroad had numerous references to The Wizard of Oz. (Always applicable to Nanny Ogg: She had red boots, she got a house dropped on her, short people showed up to take the red boots from the witch the house dropped on...)
In Death and Diplomacy, the Czan sergeant is a clear pastiche of Sergeant Major Williams in It Ain't Half Hot Mum, to the point that at one point he responds to "Is you soldier boys?" by claiming to be a concert party. The villains result in several shout-outs to Saturday morning cartoons, at one point setting up a death-trap disguised as a village of happy Smurf-like creatures. At the end of the book, when it's revealed the villains are evolutionary-enhanced Gallifreyan rodents, one of them asks what they'll do now; another rants "We do what we always do, try to take over the universe!"
According to Godengine, the standard Adjudicator method for a single person to take over a building occupied by the enemy is known as the McClane Protocol.
In Love and War, Ace accompanies New Age Traveller Jan on a cyberspace-enhanced Vision Quest, in which they meet The Trickster. Ace starts to identify who she sees him as, but gets interrupted. However his cry of "You wouldn't let it lie!" and later comment "That's a Diana and Trickster sword" makes it pretty clear he's Vic Reeves.
A Long List of the aliens and time travellers and others aided by Isaac's organisation in Return of the Living Dad includes several shout outs, since the guy delivering it is a geek:
In No Future, set in the 1970s, the Doctor watches part of an episode of Professor X, the in-universe equivalent of Doctor Who; the actor playing the Professor is not explicitly identified, but is clearly Frankie Howerd in the same comic mode as Up Pompeii.
In the 50th New Adventures novel, Happy Endings by Paul Cornell, there are two Earth Reptile musicians called Jacquilian and Sanki who talk entirely in Palare, and are very much a reptilian Julian and Sandy, including one of yer actual Round the Horne punchlines.
Don Quixote: Hundreds upon hundreds of them, although many would be unrecognizable to the modern reader because of Weird Al Effect. Chapter I part I mentions Aristotle, philosopher widely regarded as the greatest abstract thinker of Occidental Civilization. Even he has no chance to make sense of the purple prose that plagued Chivalry Books. Also in the Chapter III part II, Don Quixote's opinion about history and poetry reflects the theory exposed in Aristotle's Poetics.
The Dragaera page quote on the Did You Just Punch Out Cthulhu? page is an alteration of an earlier quote said by Vlad about the House of Athyra. As their hat is being wizards, the original is likely a Shout-Out to a much-parodied quote from The Lord of the Rings, "Do not meddle in the affairs of Wizards, for they are subtle and quick to anger". This line also gets referenced in Discworld on a couple of occasions. Once, when Vlad is warned that a sorcerous adversary could turn him into a newt, he replies, "I'd get better". Also, the most recent book, Jhegaala has a Shout-Out to Nero Wolfe- Vlad is bedridden and is using his familiar, Loiosh as his "legs". He comments that this could work well as an arrangement, leading Loiosh to comment that Vlad would soon end up several hundred pounds heavier.
"I'm referring to the strange action of the bodyguards at the assassination attempt." "But the bodyguards did nothing at the assassination attempt." "That was the strange action."
The Dresden Files have a lot of shout-outs, from Thomas being a Buffy fan to a short exchange between two characters about the medical uses of superglue, which one of them saw in "a movie about werewolves". A long but far from exhaustive listing can be found on the main page for the series.
When she turned back to the Mirror, there were excited voices coming from it, a great green dragon leaped at them, mouth wide, fire whooshing at them, then the dragon went round the curve of the Mirror and vanished—but not before she saw the dark-clad rider perched between the delicate powerful wings. More of the dragons whipped past, all of them ridden, all of them spouting gouts of fire at something Serroi couldn’t see. They were intensely serious about what they were doing, those riders and the beasts they rode, but Serroi couldn’t make out what it was they fought.
The Eisenhorn Trilogy (Warhammer 40,000) features a scene where the titular Inquisitor recounts talking with a retired Titan Princeps (commander) named Hekate during one of his travels. Princeps Hekate just happens to be the main character of the Titan series of graphic novels.
The English Dragon: The opening paragraph of chapter 14 is a pastiche of Orwell's 1984; in this version, Winston Smith's job now involves adding ethnic minorities to old films ("Films without cultural and racial diversity had to be re-cast. It was essential - for harmony and peace - to eradicate truth.")
Needful Things also has some shout outs to HP Lovecraft. The antagonist has cocaine which he claims comes from the Plains of Leng and there's some graffiti in a parking garage that reads "Yog-Sothoth rules." Also, his name is Leland Gaunt; Night-Gaunts are a fictional race in Lovecraft's work.
In the novel The Fires of Paratime by L. E. Modesitt, Jr. (published in 1982), the Immortals can travel nearly instantaneously in space and time, but they have no native technology and are forced to pilfer it from various technologically-advanced cultures throughout galactic history:
Star mentions a road made of yellow brick and Oscar says "Just don't make a hobbit of it.", referring to The Wizard of Oz and The Hobbit.
The Never-Born creature Oscar fights a duel with has a huge nose, is a superb swordsman, likes to sing poetry while fighting, and claims to have written a book, traveled to the Moon and had a house fall on him. Although he never tells Oscar Gordon his name, he's clearly based on the Real Life person Cyrano de Bergerac.
In Daphne's dream universe, a major character is a prince named Shining. While apparently she didn't intend it as a Shout-Out, her husband, the protagonist, is named Phaethon — which means "Shining."
In the Gone series, most of the place names seen on the map are references to works or TV shows related to the themes of the series, such as Stefano Rey National Park (Stephen King— Under the Dome), the Santa Katrina Hills (K. A. Applegate —Grant's wife), Grant Street (Michael Grant —Gone), Golding Street (William Golding— Lord of the Flies), and even the town name of Perdido Beach (LOST).
The illusion Penny uses on Quinn is the monster from Cloverfield.
In the first book, Mary reads the kids The Buffalo Storm, which is a book that K. A. Applegate, Grant's wife, wrote.
The fact that the visitor's entrance to the Ministry is an old broken telephone booth with the phone that should not work being located in a garbage dump is one to the pilot of Doctor Who, where Ian and Barbara find an old, broken police telephone booth with a phone that should not work in the Foreman garbage dump.
Redwall has a line about a rat named Wormtail losing a paw. Possibly coincidental, as the resemblance of a rat's tail to a worm is easy to come up with.
C. S. Lewis himself used various names which are alike or very similar to some Middle-earth names. The Space Trilogy main character, Ransom, is also a philologist and the Martian languages bear a certain similarity to Elvish.
Tolkien made several self-Shout Outs in his work, arguably, quite apart from the myriad in-universe references to 'older' tales: not expecting his 'ancient histories' of Middle Earth (which often genuinely were written much earlier) to ever be published when he was writing The Lord of the Rings, he occasionally recycled names from his existing mythology into the latter. These would have remained private S.O.s, but for The Silmarillion appearing decades later and highlighting them - as well as throwing up odd inconsistencies such as a name migrating from one race to another (e.g. Denethor, Gothmog; some instances were retconned in supplementary works as in-universe Shout Outs where the later users were said to have taken their names from heroes of old - or of the The Silmarillion character Glorfindel, whose First Age death was retconned via a one-off offscreen miracle to retrospectively make him possibly/probably the same person as the LotR character of the same name.
All of LOTR's 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 William Shakespeare in this scene. 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. Of course, the trees do come to the castle when Macduff's army uses their branches as camouflage, just as the Ents come to Isengard, and Macbeth is killed by a man who was not born, but removed from his mother's womb, just as the Witch-King, who can be killed by "no living man," is killed by a woman.
The ents marching to Isengard is more of a Take That to Shakespeare than a Shout-Out. Tolkien always hated the fact that the wood which came to Dunsinane was just men in disguise, so he wrote a scene with a real marching wood.
In "Brisingr", Arya doodles something about a lonely god in the sand in reference to "Doctor Who". Paolini mentions this in the afterword. He says he did it because he's a fan of the doctor. "And to those who got the line about the lonely god, all I have to say is that The Doctor can be anywhere at any time, even alternate dimensions. Hey! I'm a fan too!"
Eragon: "What does it mean?"
Arya: "I don't know."
In "Inheritance" there's another Doctor Who reference. Angela, the herbalist, is knitting a blue hat with runes around the edge. When asked what the runes say, she responds: "Raxacori—Oh, never mind. It wouldn't mean anything to you anyway." There is a planet in Doctor Who called Raxacoricofallapatorius (it's where the Slitheen come from.)
The name of the first ever bonded dragon, which is Muad'Dib spelled backwards.
In Paul Robinson's Instrument of God, which is a story about an Afterlife run inside a computer system, the dead people who go to orientation are given references to movies about their situation, including The Matrix, Vanilla Sky, Total Recall (1990) and What Dreams May Come. The Preface to the book mentions other stories including Robert A. Heinlein's Elsewhen and Stranger in a Strange Land, as well as The Green Mile. Also, when Supervisor 246 is explaining to a character it might not be a good idea to mention that he's from an Afterlife in another world, she agrees with him, realizing people would think she's crazy. 246 then thinks about the scene where Avery Brooks in Deep Space Nine is trying to convince the men of a mental institution that he's actually a Starbase captain.
The Jakub Wędrowycz stories have quite a lot of references, mainly to pop culture: the protagonist Badass Grandpa villager has eaten stew from some octopus-like thing named Ktulu, stole a wand from some snotty bespectacled brat with a lightning on his forehead, and is said to have also eaten some yellow thing that wandered into his yard calling itself "Pikachu". Another example is when he comes across a zeppelin, made from a metal lighter than air - his friend explains that it's an invention of one "professor Geist", a reference to the classic Polish novel The Doll.
In the book Jeremy Fink and the Meaning Of Life by Wendy Mass, there seems to be either an accidental Shout-Out or simply a very subtle one, as Life The Universe And Everything are mentioned a few times in that exact phrasing.
In the denouement of Matthew Stover's Jericho Moon, Kheperu tells Barra several Blatant Lies about how he'd gotten himself, the MacGuffin, and her back to the city after she was knocked out. Among these obvious whoppers is one where they're scooped up and carried to safety in the nick of time by giant eagles.
Too Many Magicians, by Randall Garrett, contains a Shout-Out to the Nero Wolfe novels by Rex Stout. The Marquis of London is clearly modelled after Wolfe, from physical appearance to his refusal to talk business over a meal. His assistant, Lord Bontriomphe, is an even clearer reference to Wolfe's assistant Archie Goodwin. Their chef is named Frederique (Fritz Brenner) and the senior police officer is Chief Master-at-Arms Grayme (Inspector Cramer). The title itself is a reference to three Wolfe novels with the Too Many X format.
On the other hand, while the Marquis is as smart as his cousin, Lord Darcy, he's a Brilliant but Lazy government official, not a detective, who when faced with a murder gets his cousin involved. This suggests another influence was Wolfe's alleged uncle, Mycroft Holmes, fitting in with Darcy's similarities to Sherlock.
In the same book the symbol of the King's Messengers is a lens of grey glass, which glows in the hand of the right man, created by the great magician Sir Edward Elmer; a Shout-Out to E. E. “Doc” Smith and the Lensman books.
And there's a character called Tia Einzig, a defector from the Polish Hegemony whose Uncle Neapeler escaped with the help of a Manxman named Colin MacDavid and is now living on the Isle. "Einzig" is German for "only", so Neapeler Einzig, the uncle from Man, has a name that translates as Napoleon Solo, while MacDavid's name is a simple rearrangement of David McCallum.
The same book has this exchange, which is nearly identical to the "dog in the night-time" one from the Sherlock Holmes story "Silver Blaze":
"I should like to call your attention to the peculiar condition of that knife."
Master Sean frowned. "But... there was nothing peculiar about the condition of that knife."
"Precisely. That was the peculiar condition.
The Lord Darcy stories have a lot of this stuff. Another is a clear parody of Murder On The Orient Express, in which a Hercule Poirot Expy comes to completely the wrong solution (but the same one Agatha Christie used), while Darcy comes up with the real solution undercover as an unassuming priest named Father Brun.
A couple of others feature a secret agent named Sir James le Lien (Lien = contract = Bond).
Shaun Tam referenced a few artists in his illustrations for The Lost Thing.
The Mediochre Q Seth Series has many, most of them intentional in-universe because Mediochre is a bit of a nerd. Of particular note: The university at which Mediochre and Joseph word is St Merlin's ("differentMerlin"); the Prime Minister of Mantically Aware Britain is named Kathryn Queen, colloquially called Queen MAB; one of Mediochre's catchphrases is "I love it when a plan comes together"; Joseph responds to the tempomancer's insistence that "Time is relative" with "Lunchtime doubly so?"; and in a particularly impressive one, Mediochre mentions while captured that the chances of escape are roughly equal to the odds of Kitty Pride being a real person - which seems like he's admitting defeat unless you happen to know that the character of Kitty Pride was named after a (still living) artist from Real Life, thus making her odds of being real 100% certain.
In City of Glass, Max is also seen reading Angel Sanctuary, a manga about a reincarnated angel who is in a romantic relationship with his sister. It has a case of Does This Remind You of Anything as well as bringing to question why a nine year old with fairly strict parents would be reading it. But then again, his parents have quite a lot of marital issues. So his reading choices likely passed largely unnoticed. Besides, they probably thought that that something called Angel Sanctuary would be clean and proper.
Happens often with animanga, given that Simon is characterized as a typical Geek. At one point Clary asks him if he wants to spend the evening with her watching Trigun.
Name Of The Wind has a brief, blink-and-you'll-miss-it reference to Firefly when the main character travels to the "Eavesdown Docks". Patrick Rothfuss, the author of NOTW, is an acknowledged fan of Joss Whedon.
He included another blink-and-you'll-miss-it Firefly Reference in The Wise Man's Fear when a possibly-gay (actually bisexual) character is referred to as "Sly".
A ballad's main character turns out to be not a woodcutter but a butterfly who couldn't manage to dream of a Chinese philosopher.
Tom Holt's Only Human features something of a Terry Pratchett Shout-Out, in which a man sentenced to Ironic Hell for complaining to authors that their new stuff wasn't as good as their old stuff...was forced to read the same book over and over again for the rest of eternity. His final line was that he'd just gotten up to the part where "the tourist has just met the wizard".
Pale Fire by Vladimir Nabokov has a Shout-Out for all comers. The eponymous poem's third canto has a Shout-Out to The Brothers Karamazov. The commentary to one of the lines mentions how a Hurricane Lolita has recently passed over New Wye. Charles Kinbote proposes calling the poem Solus Rex, a reference to one of Nabokov's short stories. There's a minor character named Pnin, which is also the name of one of Nabokov's other novels. Various authors and poets are mentioned, discussed, discarded at length by one of the novel's Unreliable Narrators.
The books also have a character called Will. Will's namesake is a shout out to a certain play write and poet who, in universe, was said to also be a son of Apollo.
In Peter Pan Captain Hook says he's "the only man whom Barbecue feared, and Flint himself feared Barbecue". Flint and Barbecue (better known as Long John Silver) are the leaders of the pirates in Treasure Island.
Zee Rose's The Princess 99 makes several shout outs, usually through Skye who is probably from our world though Professeur Sweet does make a Harry Potter shout out: "Unlike in the Non stories, besoms are not for riding. I repeat: do not try to ride a besom. I cannot tell you how many students have wound up with broken legs and arms because of this mistake."
A trilogy of Warhammer 40,000 novels are entitled Ravenor, Ravenor Returned and Ravenor Rogue; a rather highbrow nod to John Updike's equally alliterative "Rabbit" series (Rabbit, Run, Rabbit Redux, Rabbit is Rich, Rabbit at Rest and Rabbit Remembered).
The protagonist of David Weber's Safehold series is named Nimue. When she has to get a sex change in order to fit into the patriarchal society of Safehold, she takes the name Merlin. Later, Merlin gives Prince Cayleb a sword that is made of advanced materials, which he names "Excalibur".
In the short story "Same-Day Delivery" by Desmond Warzel, the phrase "blue bolts from the heavens" appears twice; this is a direct Shout-Out to first-edition Advanced Dungeons & Dragons; specifically, the Dungeon Master's Guide.
In Richard Peck's novel Secrets at Sea, one character mentions an ancestor in passing named Katinka Van Tassel, which is the name of the young woman Ichabod Crane loves in "The Legend of Sleepy Hollow" by Washington Irving.
Fyre, the last Septimus Heap book, contains at least contains two:
One is to the Harry Potter series, with an Ordinary Wizard named Bertie Bott being among the deceased.
Another is made by Hotep-Ra, referencing the Famous Last Words of Captain Oats, one of the men on Scott's Antarctic expedition.
Hotep-Ra got out of his chair and said to his Apprentice, Talmar Ray Bell, "I am just going outside. I may be some time." Talmar looked horrified. "Don't say that!" Hotep-Ra smiled at his Apprentice. "Why ever not?" "It's bad luck," she said. "Someone said it once and never came back." "I'll be back," said Hotep-Ra. "Someone said that once too."
In Sharpe's Tiger, Sharpe briefly sees (and is warned not to steal) the Moonstone from, well, The Moonstone.
Peter David's Sir Apropos of Nothing contains a shout-out to The Last Unicorn by Peter S. Beagle. When Apropos and Princess Entipy encounter a herd of unicorns, Entipy cautions Apropos, "You must never run from anything immortal, it attracts their attention." This is word for word what the Unicorn told Schmendrick to discourage him from running from a harpy.
In the first book, when Vince's date opens the trunk of his car and finds Jimmy the Rat unconscious and bleeding (Vince is, after all, the titular mob prince), the only response the horrified Vince can think of is "a line from that old parrot sketch from Monty Python": "He's not dead, he's resting."
The short story "Bacon" from the anthology Strange Brew contains one for The Dresden Files:
"Actually, a girl can't make a living at full-time sorcery anymore," Kathy [a witch] said with a brave smile. "Not with so many of the supernaturals trying to do things the official, human way. The only sorcerer who's gone public is in Chicago, and I hear he's struggling."
Later, he gives a more thorough one to Jewel Staite by putting a "Catalina City" on a moon of Saturn.
In the Star Trek: Enterprise novel The Romulan War: To Brave the Storm, the character of Trip at one point calls himself "Michael Kenmore" which is a Shout-Out to Stargate Atlantis, where the actor for Trip, Connor Trineer, played Michael Kenmore, the rogue Wraith turned human.
The Novelization of Star Trek II: The Wrath of Khan contains an extended in-universe Shout-Out to Lewis Carroll, as two of the scientists on the Genesis Project discuss the discovery of the sub-elementary particles they named "snarks" and "boojums". Just as quarks come in different "flavours" with odd names like "strange" and "charm", snarks and boojums are sorted by "five unmistakable marks" which the scientists call "taste", "tardiness", "humor", "cleanliness" and "ambition" ... all straight from Fit the Second of the nonsense poem. (The scientists names, incidentally, are Madison and March.)
And in the Star Wars novels, Han, and later Corran Horn, have used the fake identity "Jenos Idanian", an anagram of Indiana Jones.
Death Star has a conman who's managed to sneak on board the Death Star setting up a fake ID under the name of Teh Roxxor.
In Swords of Exodus, the sequel to Dead Six, the commanding officer for Mike Valentine when the latter was in the US Air Force, was Colonel Christopher Blair, the Player Character from the Wing Commander game series.
Mercedes Lackey pulls off a clever one in her book The Fairy Godmother. Her protagonist Elena goes to a Hiring Faire, and is the second-to-last person hired. The last person in the square, when she leaves? Mort.
In Home from the Sea, also by Mercedes Lackey, characters Nan and Sarah mention that they were helped out in Egypt by a woman who was called Sitt Hakim by the native people. That plus the rest of her description puts her as Amelia Peabody.
Star Trek: Human habitable worlds are called M-Class (with a note that it was so embedded in popular culture at the beginning of space travel that scientists just went along with it), while an apparently unwinnable training scenario is called 'a Kobayashi Maru'
In the BIONICLE book Time Trap, the Shadowed One responds to the notion of cutting off hands as punishment for failure with the line "I think enough hands have been removed this year", a reference to Star Wars's fondness of having its characters lose their hands, and specifically to the movie Revenge of the Sith, which came out the same year as the book.
The children's picture book The Tobermory Cat by Debi Gliori includes a picture of Tobermory bookshop in which all the books in the window are other picture books about cats, including Goodbye Mog by Judith Kerr and Fred by Posey Simmonds.
Cryoburn has two: Miles thinks to himself "Imperial Auditor Vorkosigan; Threat or Menace" (in Spider-Man, J.J.J.'s paper, The Daily Bugle often ran headlines "Spider-Man: Threat or Menace?"). And Armsman Roic quips to a local "Don't worry, I have a license to stun." The local responds "I thought that has a license to kill?" Both, of course refer to James Bond's 00 "License to Kill".
The authors of Warrior Cats have admitted to sneaking in quotes from Rambo. Also, the second arc was original going to be named The Next Generation, after Star Trek. The magazine "Cat Fancy" appears in a panel in one of the mangas, and "Here Comes the Sun" is the name of a chapter in a Dungeons & Dragons-style game in the back of the books.
Sideways Arithmetic From Wayside School, Wayside's think outside the box puzzle book, features in the first chapter a series of prototype algebra problems where numbers are substituted with letters. The first such problem is ELF + TOOK = FOOL.
Welkin Weasels runs entirely on Shouting Out to various famous literature, movies, and historical events, often with an Incredibly Lame Pun or two mixed in. (See the reference to Treasure of the Sierra Madre and/or Blazing Saddles as the Talking Animal marmot sheriff faces off with an outlaw: "Badgers? We don't need no stinkin' badgers!")
The Wild Cards series has the Indio-Irish Elephant Girl, whose real name is Rhada O'Reilly (c.f. Radar O'Reilly in M*A*S*H).
Also a Potter reference, in one of the books is a helping robot, called a "house elf", which is named Dobby, IIRC.
The city that Blaine is in constantly plays a series of drums which Eddie mentions sounds suspiciously like a ZZ Top song.
EVERY Steven King book EVER has a long list of obscure to vague shout outs to his sixty other 900-page books.
As is probably to be expected from a series about a consciousness forming and awaking in the internet, the WWW Trilogy is chock full of references to past films and novels that have dealt with the concept of AI, mostly in the form of title-dropping.
In High Wizardry, a man apparently fitting the description of the fifth Doctor saves Dairine from the servants of the Lone Power chasing her.
HP Lovecraft was ridiculously fond of shouting out to his other works to the point where most of the time it didn't really make any sense. The names just happened to be the same. Also, he and his circle of author friends absolutely loved shouting out at each other and shared several eldritch deities.
The founder of the Pickman foundation is presumably NOT the Pickman of "Pickman's Model". Lovecraft's stories tend to take place in the same small part of New England, and often concern the same kind of ladies and gentlemen from old, old families (so they can have old, old secrets). Hence, the same surnames turning up again and again is actually fairly realistic: the oldest families have a fair number of members by now, and they are fairly important to local history as well.
John Ringo tends to throw tons of shout outs to various things his works, including but not limited to:
A recurring character in Robert Rankin's books is the "psychic youth and masturbator" Danbury Collins. This is based on Andy Collins, author of dubious New Age work The Knights of Danbury and a rival of Robert's.
In Green Smoke by Rosemary Manning, Susan suddenly wonders if you need to be formal when talking to a dragon, remembering a book that said you should address a cat as "O Cat". (When she addresses the dragon as "O Dragon", he corrects her; he's R. Dragon.)
In the Rihannsu novel The Empty Chair Gurrhim tr'Siedhri comments that it will be better for the rebellion if he remains Legally Dead for the moment because his heirs will maintain control of his considerable wealth and corporate resources, which can then be used to help the Free Rihannsu. Leonard McCoy then makes a snide remark about Gurri staying dead for tax purposes.