Michael Grant co-wrote the Animorphs series with his wife, K. A. Applegate and transplanted the character of Marco into his new novel series Gone as Edilio. Both characters are short Hispanic youths with dry wits who are remarkably competent despite their laidback natures.
Not to mention Dekka is Tate from Remnants except younger. The characters of Caine and Diana are reminiscent of Yago and 2Face from the same series respectively.
The whole point of the Meg Cabot novel Avalon High, where all the major characters are revealed to be reincarnations of King Arthur legend. The main character, Ellie, is originally thought to be the reincarnation of the minor character Elaine, the Lady of Shalott but is revealed to be the much more important Lady of the Lake.
In the Beauty Trilogy, by Anne Rice, the character of Laurent is exactly the same as Lestat, minus the vampirism.
Laurence Kirkle in Beyond the Western Sea has a character arc that's very similar to Charlotte's in The True Confessions of Charlotte Doyle.
Children's author Bill Peet started out as a Disney cartoonist and a degree of expyness can be seen between Dumbo, whom he created and the title character of Chester The Worldly Pig. Both begin lives at the circus on a bad note, mocked by the audiences and ill-treated by clowns, but later achieve happiness and success there through an extraordinary talent (flying with ears/body coloring which looks like a map of the world)
Loren D. Estleman's Claudius Lyon invokes and parodies this trope with regards to Nero Wolfe; Lyon is a Hero-Worshipper of the more famous detective and has sought to emulate his life as closely as he can within his own abilities and without being sued. However, Lyon — while not incapable — is not quite as good as Wolfe, meaning that things frequently get a bit skewed in translation. For example, while Wolfe is famous for growing orchids in his rooftop greenhouse, Lyon lacks a green thumb and so has to make do with growing tomatoes instead, because they're easier to grow.
The Vord are a race of insect-like creatures that have specialized sub-breeds for different combat roles, share a sentient hive mind, can infest humans to take over their bodies, and are dependent on a waxy substance that they smear across the ground in their nests. They also have a four letter name, the third letter of which is R, though that similarity to the Zerg was probably coincidental.
The Culture tends to feature among its protagonist one of two types (sometimes in the same novel, often as semi-romantic interests). If female, they will be a sexybisexual operative accompanied by a snarkyDrone companion. If male, they will be a badass mercenary, who is usually from outside the culture, but ends up (sometimes reluctantly) aiding them. Given a bit of a twist in Surface Detail in which there are two male mercenary characters, one of which is a former lover of the female protagonist (of the sexy, drone-paired ilk), and the other of whom is revealed in The Stinger to be a character from a previous novel under an another alias.
Daystar has a number of expies of Biblical characters:
Tiala Caldwell, of Mary, as she is the virgin mother of the promised Word to Come (Boh-Dabar), who will restore his people. The previous book in the series established her as faith-filled and devoted to the Eternal Speaker, paralleling Mary's best-known trait of faith.
Tavkel Caldwell, of Jesus, as he is the Boh-Dabar, living expression of the Eternal Speaker, who comes to take darkness from all people and remake and restore the world to perfection. He lived a perfect life and died to bring spiritual renewal and redemption to all.
Kinnor Caldwell, of Lazarus, having been raised from the dead in front of his relatives to show Boh-Dabar's power and authority over death.
Subverted with Kiel Caldwell, who does not, in the end, become an Expy of Caiaphas. He begins to head down the path of opposition to Boh-Dabar, trying to turn people from Boh-Dabar, but he realizes his mistake, repents, becomes a follower of Boh-Dabar himself, and tries to undo the damage he had done.
The Discworld series rarely goes for long without a Shout-Out that might become an expy, for purposes of parody, satire, or fun, as Terry Pratchett knew his predecessors, and wrote enough books that he was full capable of expy'ing himself.
For example, Equal Rites has an Archchancellor of Unseen University who is clearly a first draft of the later Archchancellor Ridcully, particularly as both have somewhat romantic relationships with Granny Weatherwax.
We are introduced to about five suspiciously similar versions of Cut-Me-Own-Throat Dibbler, Sergeant Doppelpunkt and Corporal Knopf (Colon and Nobbs) show up in The Amazing Maurice and His Educated Rodents, and Igors are Expies of each other.note Literally, in case that wasn't clear. One of the defining characteristics of an Igor is that he has parts of several other Igors (or somebody else) stitched onto his body to replace missing/faulty parts. When an Igor says he has his father's eyes, he means it.
The non-Discworld Good Omens features a Death who is similar in many ways (though far from identical) to the Discworld's Death. For instance, he speaks all in small caps. And it's possible to see Aziraphale as something of an expy of Carrot from the Discworld "Watch" books- both are extremely idealistic characters who rather than being the Wide-Eyed Idealist, are rather clever, even cunning.
In Wintersmith, Anoia the Goddess of Things that Get Stuck in Drawers has exactly the same personality (and chain-smoking habit) as Adora Belle Dearheart in the books about Moist. She's also heavily implied to be the deity formerly known as Lela the Volcano Goddess ("the Storm God keeps raining on her lava"), who was explicitly compared with Adora Belle in Going Postal.
First Mate Cox in the non-Discworld Nation is exactly the same kind of Ax-Crazy as Carcer, down to sharing some of the same dialogue. Andy Shank is also described like this.
Brutha from Small Gods might be an expy (or at least extended shout-out) to Severian of Book of the New Sun. Both of them are big guys with Photographic Memory who grow up in monasteries of a weird Crystal Dragon Jesus religion. Pratchett seems to acknowledge the similarity in having one of the people Brutha meets named Severian. On the other hand, Pratchett claimed to find the New Sun series unreadable, so this may just be coincidence.
Mrs Tachyon in the non-Discworld Johnny and the Bomb has the same manner of speaking as Foul Ole Ron. Thankfully, the Smell of Foul Ole Ron does not get an Expy.note It is alluded to, though: it is remarked that Mrs Tachyon when in hospital struggled magnificiently against the idea of a very necessary bath.
The clearest shout-out of all, though, is to an outside source, and occurs in the first chapter of the very first Discworld book, when a great fire in Ankh-Morpork is watched by Bravd and the Weasel. The series may have evolved away from genre fantasy, but Pratchett was very clear where it started.
The same book sees a sentient Black Sword which is capable of speech and of sucking the very soul from its victim.note Being spoken at by a boring tinny monotone metallic voice does this to people.
A civilization known as The People, present in several Doctor Who novels, is obviously based on Iain M. Banks' The Culture.
Given that Fangirl is a loving parody of real-life fandoms, it's not shocking that a couple of these show up. The world that Cath writes her fanfiction about is a general expy of the Wizarding World, with her favored pairing standing in for Draco/Harry.
In the book Fat Kid Rules The World, the protagonist's friend is a punk rock guitar god named Curt Maccrae. Sounds familiar.
A lot of characters in Fifty Shades of Grey are similar to their original Twilight templates, with some characteristic of movie actors mixed in: Ana is a clumsy virgin who bites her lip a lot and has an absent-minded mother. Christian is an orphan adopted into a rich family, one of his adoptive parents is a doctor, he plays piano and has a brother and a sister whom Kate and Ethan Kavanagh, blonde siblings, hook up with respectively. Etc ad nauseum.
Anthony Bourdain's Gone Bamboo features, as well as Mary Sues of himself and his then-wife, a few characters from his earlier A Bone in the Throat. In at least the first British edition of the later book, their names are the same as in A Bone in the Throat, in American editions, they have been changed, e.g. "Charlie Wagons" becomes "Donnie Wicks".
Joel Rosenberg transplanted the characters of Durine, Kethol and Pirojil from his Guardians of the Flame series into the novel Murder in La Mut, which he co-wrote with Raymond E. Feist. The whole book is basically an excuse to put Rosenberg's characters in Feist's world for one novel and let hilarity ensue.
½ Prince has a rather blatant expy to Kenshin. In case the red hair, scar, expert swordsmanship, and clothes weren't a big enough giveaway, they even name the character Kenshin.
Piper's father is mentioned to have played The King of Sparta and there is mention of The Poster which the two considered funny until it hit the internet.
There are several similarities between Annabeth and Reyna, the praetor of Camp Jupiter, in The Mark of Athena. Annabeth immediately notices some of them when she first meets her.
Both are considered the female leaders of their respective camps and are highly respected by their fellow campers.
Both have or were going to have a romantic relationship with the male leaders of their camps: Annabeth has one with Percy, while Reyna would have had one with Jason if he hadn't been kidnapped by Hera/Juno.
Both refuse to believe the worst has happened to their significant other. Annabeth is out searching for Percy throughout The Lost Hero, while Reyna refuses to hold an election for Jason's replacement as praetor despite others' pestering her for it, as she believes Jason is still alive.
Both of their love interests (Percy for Annabeth and Jason for Reyna) have a problem of being unable to pick up on Annabeth and Reyna's emotions or feelings.
Both of their love interests denied or deny an attraction to them. Percy doesn't realize how much he loves Annabeth until The Last Olympian, while Jason repeatedly tells his girlfriend Piper that he never was in love with Reyna. Despite Jason saying this, after he reclaims his memories in The Lost Hero, his memories of Reyna make him question his feelings toward Piper.
Both were involved in a love triangle with their love interest: Annabeth was in a love triangle with Percy and Rachel Elizabeth Dare in The Battle of the Labyrinth and The Last Olympian, while Reyna was in a love triangle with Jason and Piper McLean in The Mark of Athena, although Jason states that he never felt that way towards Reyna, even though Piper believes otherwise.
Both have been on a quest with their love interest; every quest Annabeth ever went on was with Percy (with the exception of her mission to reclaim he Athena Parthenos from Arachne) while Reyna and Jason once visited Charleston, South Carolina on a quest together.
Both are forced to hold an expression of fearlessness in public to prevent spreading panic throughout their forces. Annabeth even notices this whenever she first meets Reyna in The Mark of Athena, and it is implied Reyna notices this as well.
Both are very good at reading others' emotions and deducing motivations and/or feelings, while also hiding their own.
Both have a fondness for architecture, as they both were seen admiring New Rome in The Mark of Athena.
Both have knowledge of the others' culture, and do not judge them for it.
Both are the children of a war goddess; Annabeth is the daughter of Athena, the Greek goddess of wisdom, war, and battle strategy, while Reyna is the daughter of Bellona, the Roman goddess of war.
Both had a crush on Percy Jackson. Annabeth states that she has a crush on Percy since they first meet when they were twelve, while Reyna attempts to convince Percy to become praetor and become her "friend", which both Percy and Annabeth interpret as Reyna making a move on him.
Both visited Circe's Spa and Resort in the Sea of Monsters and met the other while they were there; Annabeth and Percy visited the Spa while looking for the Golden Fleece, and Reyna was one of Circe's assistants at the Spa and Resort. The two met while there; Reyna was one of Circe's attendants who combed Annabeth's hair and gave her a makeover.
Both are considered scary by a demigod of the prophecy; Hazel and Frank are both somewhat intimidated by Reyna, while Leo has been scared of Annabeth ever since they met at the Grand Canyon while wearing her "give me Percy Jackson or I'll kill you" look.
Both ran away from home; Annabeth ran from her father and stepmother's house in San Francisco after being attacked by spiders for three nights in a row, while Reyna and her sister Hylla ran away from San Juan and became Circe's attendants at her spa.
Intra-series example: In the Warhammer 40,000Horus Heresy novels, both Saul Tarvitz and Nathaniel Garro sort of come off as expies of Garviel Loken...
The four children of In the Keep of Time are in many ways quite similar to the four Pevensies of Narnia. At the start, Andrew is dismissive of his younger siblings and not particularly excited about their stay in the country, and he is also the first to adapt very well to the past and become immersed in the time period and even a warrior mentality, like Peter; Elinor is the one most skeptical about the reality and acceptability of the adventure, as well as the Team Mom, like Susan; Ian is very much resentful and jealous of his youngest sister; and Ollie herself is the one whose recklessness and eager curiosity leads them into the past in the first place. However, they all eventually grow beyond these roles, with Andrew rejecting the past world for the present, Elinor becoming stronger and more willing to believe in the impossible, Ian not betraying them like Edmund did, and Ollie ends up losing herself and has to be taught and bonded with her siblings before she can recall who she is—which may perhaps be a commentary on Lucy's being thought mad and how incredibly willing she was to believe and immerse herself in Narnia.
Legacy of the Dragokin: Benji is like version 2.0 of the previous Draconica protagonist, Ben. He's a supporting protagonist without combat skills that follows the heroes and gets an 11th-Hour Superpower. The key difference between them is Benji doesn't say Shout Outs to real world products.
The Lunar Chronicles draws visible influence from Sailor Moon, and while most of the details of characterization have been mixed up and blended with other elements, there are a couple of characters who are pretty much direct exports:
Prince Kaito of Earth's Eastern Commonwealth, handsome and charming yet Adorkable and prone to playfully teasing the object of his affections, is recognizably based on Mamoru Chiba and Mamoru's past life Prince Endymion, a prince of Earth who forms a star-crossed romance with a princess of the Moon while being targeted by a malevolent, mind-controlling sorceress-queen.
Scarlet Benoit, meanwhile, is an expy of Makoto Kino: curly-haired, statuesque, fierce and almost suicidally brave when her strong sense of justice is provoked or her loved ones are threatened. She and Wolf also bond over food on a couple of occasions.
Onimi from the New Jedi Order series of Star Wars, is essentially the Star Wars incarnation of Kefka Palazzo from Final Fantasy VI, in personality, position, as well as backstory. Essentially, before the events of the book started, Onimi used to be a mere shaper, like how Kefka originally was an average human being. However, both characters did a ritual/experiment that greatly deformed them, and yet at the same time resulted in being infused with the ability to utilize magic/the Force. It is also heavily implied that the same thing that resulted in their deformation and the origin of their powers also resulted in them becoming insane and being demoted to being a court jester. Likewise, both also desired to become a god for no reason outside of just out due to their insanity, and also manipulated their ruler and the empire into helping them.
Speaking of the New Jedi Order series, the Yuuzhan Vong bear more than a few similarities with the Imperium from Warhammer 40,000. Their society is defined by religious fanaticism. Their technology is thousands of years old and designing anything new is heresy (but that may be overlooked if it's effective). Their religion is rather sadomasochistic. Their religion commands them to commit genocide against the rest of the galaxy.
For the new Star Wars continuity, Rae Sloane is shaping up to be an expy of Gilad Pellaeon. It's now established that she was the ranking Imperial officer who ordered the retreat from Endor, and now that the Empire is collapsing around them, she is becoming the trusted subordinate to a mysterious fleet admiral who has an appreciation for classical music.
In Blackout by Mira Grant, the character Dr. Kimberley, who uses the alias Dr. Shaw for a while, is pretty clearly based on Dr. Liz Shaw from Doctor Who.
Jamie Fraser, the hero of Diana Gabaldon's Outlander novels, has been acknowledged by Gabaldon herself as being based on Doctor Who companion Jamie McCrimmon, who was played by the actor Frazer Hines.
Captain Arthur Hastings from Agatha Christie's Hercule Poirot series is obviously based on Dr John Watson. Both serve as the First-Person Peripheral Narrator to their Great Detective companions, both were had military backgrounds and got injured at some point, both have exceedingly transparent countenances and thus cannot be trusted with discretion, both are weak to the female charms, both are highly imaginative and cannot properly connect the dots when they find clues to the mysteries.
The characters in Project Itoh's Harmony are Gender Flip versions of characters from Metal Gear Solid 4, the novelisation of which he was writing at the time. Notably, Miach is Liquid Ocelot as a Japanese schoolgirl.
The three major characters of Roz Kaveney's Rhapsody of BloodUrban Fantasy series, Emma, Caroline, and Mara, are at their first introduction blatantly inspired by Cassie, Thelma, and Ella of Hex. They quickly diverge from this, however, thanks to getting older than (apparently) teenage, being all three of them lesbians, and being actually good at the whole "fighting supernatural evil" thing.
Intra-universe example: Terry Brooks's Shannara books. Essentially each set of main characters, as they are successively descended from each other, differ little from their ancestors. (The plot lines are even more similar than the characters.)
Sisterhood Series by Fern Michaels: Charles Martin is totally an Expy of James Bond. He is British, he spent time working for MI-6, and is definitely a spook. Unlike Mr. Bond, however, Charles mostly does the planning and pulling various strings. That, and he is at least 60 years old.
This is lampshaded (as so many tropes are) in the Thursday Next books; a minor character mentions offhand that two literary characters seem very similar. In fact, they are the same character, but Thursday doesn't try to enlighten the speaker on the "economies of the Book World."
Emily Rodda's The Three Doors trilogy, which takes place in the same universe as  takes the trio from the original series and pretty much recycles them in the trilogy.
Rye is an expy of Lief - both characters are 16 year old boys who are given a magical object to help them on a quest but don't know precisely how the magic works. Both have speed and agility as one of their main traits.
Sonia for Jasmine - Wild girl orphans who are the same age as their companion. A lot is made of their hair colour (Jasmine's black hair and Sonia's red hair are constantly being mentioned) and both tend to speak their mind even when those around them do not approve (although Sonia is more refined than Jasmine, on the whole).
Dirk for Barda - an older male who is strong and heroic, feels responsible for the younger people and tends to favour brute force if it is an option. Both have a habit of being knocked out or seperated from the group since their strength and bravery would solve many situations that the younger two could not solve on their own. Both like to be in charge and are natural leaders, but end up deferring to the younger male against their better judgement.
The Bag of Nine Powers for The Belt of Deltora - each is given to the hero of the story without any real guidance on how to use it, the hero can use it the best while others tend to only experience the powers through the hero.
Tamora Pierce's Tortall Universe contains a god named Gainel the Dream King, whose visual description is pretty much identical to Dream. The name "Gainel" may be a play on Neil Gaiman.
The Red Knight is a lot like Mordred, born from the king's rape of his mother and intended to lead the Wild to slay his own father.
Ghause Muriens is very much Morgan Le Fay, being a powerful sorceress who conspires against the King.
Jean de Vrailly is a darker version of Sir Lancelot. He's a giant of a man who's being manipulated by "an angel" and proves himself to be the greatest knight in the world, he comes from an expy of France and has designs on the Queen.
Yoruka in Undefeated Bahamut Chronicle is practically the spitting image of Kurumi from Date A Live. Appearance-wise, they both have black hair in twintails, unnatural heterochromianote Yoruka's left eye is purple due to receiving Baptism; Kurumi's left eye is a clock due to being a Spirit and wear shoulder-bearing outfits with the colors red and black. They're both Yandere for the main character (though Yoruka ceases to be one a book after her introduction). They're both the most sensual and the most lethal out of the main cast.
Roddy Doyle's The Van mostly features the same cast of characters as his earlier The Snapper; the film versions of the two books were made by different production companies, the makers of The Snapper had the rights to use them, so the names were changed in the second film.
Brandon Sanderson says that Warbreaker's Siri and Vivenna were exported from a novel that he never finished writing. Additionally, he mentions that Denth is heavily based on La Résistance leader Kelsier from his previous Mistborn series in part to make the reveal that he's actually evil all the more unexpected.
David Eddings does this repeatedly, blatantly, and unashamedly... so blatantly, in fact, that it becomes a plot point, at least in-universe.
While H.P. Lovecraft himself largely avoided this (indeed, he's on record as wanting to break free of the tired old horror clichés that were en vogue in his time, as well as a confirmed materialist), later Theme Park Versions of the Cthulhu Mythos frequently end up looking rather like straight-up expies of the literal forces of Hell. Forbidden pacts, supernatural corruption, Things Man Was Not Meant To Traffic With Lest He Lose His .
Jodi Picoult has many of these throughout her stories, especially after the popularity of My Sister's Keeper. There is the mother of a sick child who means well but focuses on the child to the point of ignoring everyone else (Sara, Charlotte, Emma), the husband who feels that what the mother is doing is wrong but won't do anything about it (Brian, Sean), the sick child who is always wiser than their years and who often has little character development until the last chapter (Kate, Willow, Claire Nealon), the ignored child (Anna and Jesse, Amelia) and the lawyer with personal problems (Campbell, Jordan, Marin).
Almost every protagonist of Louis L'Amour's hundred-or-so-books is pretty much one of two guys:
A badass white guy from some place east of where the book is set.
An Indian Brave who is just like the Badass White Guy except that a big deal is made about his race.
Noel Streatfeild often does this with a character who is a nanny or nurse to the protagonist(s). Hannah in Thursdays Child, Nana in Ballet Shoes, Hannah in Theater Shoes, Nana in Skating Shoes, and Pursey in Dancing Shoes all have essentially the same personality (and nearly the same name—even Pursey was once a nanny, although she isn't during the book) but are not the same person.
P. G. Wodehouse lampshaded this in the preface to Summer Lightning, where he mentions a critic who claimed his last novel recycled "all the old Wodehouse characters under different names." Summer Lightning itself, the preface notes, neatly averts this by including all the old Wodehouse characters under the same names.
If you click on Robert A. Heinlein you will see listed on his page his three most common character types.
All of Tom Holt's male protagonists are basically the same person. The women get a little more variety, but not that much.
Zilpha Keatley Snyder keeps doing this. Several of her books after The Changeling feature characters who, while not literal transpositions of Ivy Carson and Martha Abbott, are certainly close relatives. Look for them in the Green-Sky Trilogy, The Unseen, and The Treasures of Weatherby. She even puts an interracial cast a la The Egypt Game into Martha's upper-crust Castle Court residence in a later series, and re-uses the name Abbott in The Bronze Pen. She is also fond of the Big Fancy House (often ancient, abandoned, falling to pieces, and in one case so horribly burned that the little girls make up a Ghost Story about it).
Among criticisms of the Colleen McCullough novel The Touch is that the character of Eleanor "Nell" Kinross is this of Justine O'Neill from The Thorn Birds, given their many similarities—an abrasive personality, unconventional, but not necessarily unattractive looks, a thorny relationship with her mother, etc.
Brutus, from The Hunger Games, is essentially Cato MKII. In fact, he and Cato's final kills were the men from District 11, both were the next to die and the last in each game, and both were killed by the volunteer from District 12 for that year.
William of Baskerville, the monastic sleuth from The Name of the Rose is an expy of Sherlock Holmes - English, preternaturally observant, phlegmatic, calculating, occasionally conceited, and he even chews a mysterious 'herb' to help him concentrate. His name is a clear reference to The Hound of the Baskervilles. His protegé, Adso of Fulk (the narrator) is the Watson of the relationship.
Redwall frequently reused character types and plots. The most obvious, however, may be Gabool the Wild, Big Bad of Mariel of Redwall and Emperor Ublaz "Mad Eyes", Big Bad of The Pearls of Lutra. Both are pirate kings who rule an island (Terramort, Sampetra) far away from Mossflower. Both command the loyalty of all the pirates of their respective seas (northern, southern). Both open their book by killing one of their captains (Bluddrigg, Conva), and then face a rebellion from said captain's brother and fellow captain (Saltar, Barranca). Both are betrayed by their trusted right hand rat (Greypatch, Sagitar) and both have a venomous tropical animal as their personal pet and secret weapon (Skrabblag the Scorpion, an unnamed coral snake). Both have little to do with the main plot, both alienate their subordinates, and both and sit on their island going mad and surrounded by a dwindling number of retainers until the heroes arrive, at which point both are killed by their respective secret weapons. The only real differences are their species and Ublaz's greater veneer of sanity.