In K.A. Applegate's Animorphs Jake's decision to "ram the Blade Ship" in the series' ending mirrors Elfangor's decision to ram an enemy ship in The Andalite Chronicles. While Elfangor won his battle involving that tactic, the result of Jake's decision is unclear.
Stephen King often inserts Mythology Gags in his novels, making brief, casual, and usually vague references to events or characters from a previous novel that might not have absolutely nothing to do with the current novel whatsoever, but that fans of King who have read most of his novels would easily be able to recognize.
For example, the novel Needful Things includes bully Ace from the novella "The Body" and references to the novels Cujo and The Dead Zone. This makes sense as all of these events occur in the same (fictional) town.
In The Dark Tower novels, elements from many of his earlier books appear, with such frequency that by the end of the series the reaction has accelerated into full-blown Canon Welding.
Dolores Claiborne is possibly the strangest example of this, as the titular character experiences a brief psychic connection with the protagonist of Gerald's Game, to whom she has no other connection at any time.
This connection happens on July 20, 1963, during a total solar eclipse, which makes it a real-life Shout-Out to an actual total solar eclipse that went across Maine on July 20, 1963.
Insomnia contains a good deal of this, including numerous references to The Dark Tower, but the one that stands out the most is when the protagonist finds a pair of shoes belonging to the little boy who died from Pet Sematary.
Pet Sematary itself contains a passage where a character mentions that it used to be legal to keep animals like raccoons as pets in the area, before there was an incident involving a rabid dog.
In The Tommyknockers, one character hallucinates Pennywise the Clown from IT while driving through Derry.
And in IT, a scene involves Dick Halloran, the cook from The Shining.
Also in Dreamcatcher, one of the main characters heads to Derry and finds the phrase "Pennywise lives" scrawled on the monument dedicated to the Loser's Club, which was the title the main children gave themselves in IT.
Desperation and The Regulators were published simultaneously (by King and his alter ego, Richard Bachman), and thus the characters, settings and plot are connected and have a lot of overlap. However, both novels also feature a character called Cynthia Smith, who mentions briefly in Desperation that her nose was broken by a bad man. Cynthia was a secondary character in King's previous novel Rose Madder, in which the assault took place.
"The Man Who Would Not Shake Hands" is another tale of the uncanny told at the same brownstone men's club in Manhattan where "The Breathing Method" takes place.
The four ill-fated kids in "The Raft" are students at Horlicks University in Pennsylvania. The Cunninghams, Regina and Michael, were professors there in Christine. (The events of "The Crate" took place there as well.)
This one may overlap with Genius Bonus. In "The Jaunt," the first man to take the Jaunt wide awake (only to emerge insane and die as a result) is a convicted killer named Rudy Foggia. As King aficionado Tyson Blue points out in The Second Stephen King Quiz Book, Rudy Foggia's initials may mark him as another incarnation of Randall Flagg; in The Stand, Flagg's aliases all have the initials "R.F." (Richard Freemantle, Russell Faraday, etc.)
The new novel, And Another Thing... opens with Arthur, Ford, Trillian and Random experiencing false lives, before learning they're still on Earth, and it's still being destroyed by the Grebulons (as seen in Mostly Harmless). When describing her hallucination, Trillian claims they were rescued from Earth by the Babel Fish, which transported them to Milliways. This was the bonus "they're not really dead" ending of The Quintessential Phase of the radio series.
The wonderfully meta introduction to said book may also count, as it alludes to the "trilogy in six parts", as well as the franchise's radio, television, film and stage productions.
Wicked, in novel form, makes a lot of minor references to the oft-ignored rest of the Baum series. Perhaps most notable is naming the deposed Ozma (there's more than one in the series) "Ozma Tippetarius": Tippetarius, or Tip for short, being the name of the gender-bent disguise of Ozma from The Marvelous Land of Oz.
The Artemis Fowl Files (a companion book) is dedicated to "Finn, Artemis's best friend." Finn is the surname of the main character of The Wish List, and also a false surname that gets used in Airman.
In the BIONICLE children's book Desert of Danger, Mata Nui first tries to defeat a sand bat by knocking off it's mask, which was a very common theme back when the toy-line first started. Another character instantly points out that in this new world Mata Nui found himself in, animals don't wear masks. Even so, the book's artist did use an older bat-themed mask as a reference for drawing the sand bat's head.
In Star Trek: Ex Machina, McCoy, exasperated by the sheer diversity of aliens on the refit Enterprise, sarcastically asks whatís next - hortas and glass spiders? Those readers familiar with the works of Diane Duane will get the joke (a reference to two of her characters, crewman Naraht and Kítílk).
Pick a Sherlock Holmes pastiche, adaptation... anything about Sherlock that Doyle never wrote. It is an absolute guarantee that there will be at least one of these.
When a subject of peoples interests come up in No Deals, Mr. Bond regarding Bond's comment to would-be defector Smolin about him having a cover name of a nineteenth century politician, Smolin mentions that some might even read the works of Margaret Drabble and Kingsley Amis, latter whom wrote the Bond continuation novel Colonel Sun.
A character in Death Is Forever complains about the use of the Textual Celebrity Resemblance trope, telling Bond that an author whose book he is reading constantly uses it to describe people. Bond then notes that someone once told him that he "looked like Hoagy Carmichael with a cruel mouth", which is how he was described by Ian Fleming in Casino Royale.
In COLD, Bond receives an audio message from his past fling Beatrice di Ricci, which icludes the phrase "I want to win. I don't want lose or die." The phrase references the title of Win, Lose or Die, the novel where she and Bond met.
Yayandas: We are about to calibrate the newly installed, super-responsive inertial damper. You will never again feel the slightest shake, and never once be torn from your sleep, even if you are rammed head-on by a Xenon. Nopileos: Rrrr... do they do that? Yayandas: So one hears...
The fourth volume of A Song of Ice and Fire mentions several statues of various gods of death in the House of Black and White, including that of Bakkalon, also known as the Pale Child. Fans of the author's other works might recognize this as the name of a deity in his "The Thousand Worlds" setting, in particular the 1975 novelette "...and Seven Times Never Kill Man!"