In the many, many books of the Dragonlance series, any kender characters that appear are similar to Tasselhoff Burrfoot, since most of the race's members seem to have the same (bizarre) personality. Most of them end up being the Alien Scrappy of that particular book, but on some writers have perpetrated subversions...
Within the Dragonlance series there are also the gods Paladine and Takhisis, who serve as stand-ins for the traditional Dungeons & Dragons deities Bahamut and Tiamat, respectively.
The authors' next series, the Deathgate Cycle, includes a pretty blatant example of this trope in the form of bumbling would-be wizard Zifnab.
Zanfib, from another Margaret Weis/Tracy Hickman collaboration.
However, it is strongly implied that Fizban, Zifnab, and Zanfib are all the same person.
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.
Half the main cast of These Old Shades by Georgette Heyer are Expys of the main characters in The Black Moth. They even have the events of TBM as backstory, and the Dukes of Andover and Avon have similar nicknames, "Satanas" and "Devil".
Pretty much every main/significant minor character in every Dan Brown book ever.
Kane in the Ea Cycle is, perhaps unsurprisingly, an expy of Kane from Karl Edward Wagner's stories.
Furthermore, a lot of people and things in Ea Cycle have direct counterparts in the same author's earlier sci-fi series.
Intra-series example: In the Warhammer 40000Horus Heresy novels, both Saul Tarvitz and Nathaniel Garro sort of come off as expies of Garviel Loken...
In the Doctor WhoEighth Doctor Adventures novel Vampire Science, the Doctor is brought into the situation by Dr Carolyn McDonnell, a highly-motivated San Francisco doctor whom he met on a previous visit to the city (as established in the prologue). Dr Grace Holloway from The Movie was Exiled from Continuity at the time.
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.
The Discworld book Equal Rites has an Archchancellor of Unseen University who is clearly a first draft of the later character Ridcully, particularly as both have somewhat romantic relationships with Granny Weatherwax. Also, it's possible to see Aziraphale of Good Omens as something of an expy of Carrot from the "Watch" books- both are extremely idealistic characters who rather than being the Wide-Eyed Idealist, are rather clever, even cunning.
Pratchett often plays this for comedy: we've been 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.
Literally, in case that wasn't clear. One of the defining characteristics of an Igor is that he has parts of several other Igors stitched onto his body to replace missing/faulty parts. When an Igor says he has his father's eyes, he means it.
Good Omens also introduces a Death who is similar in many ways (though far from identical) to the Discworld's Death.
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 Nation is exactly the same kind of Ax Crazy as Carcer, down to sharing some of the same dialogue.
Brutha from Small Gods is 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.
Mrs Tachyon in 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.
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".
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.
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.
All of Tom Holt's male protagonists are basically the same person. The women get a little more variety, but not that much.
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)
Harry Potter: James Potter and Sirius Black's young, teenage selves as seen in the 800-word prequel JK Rowling wrote for charity are completely interchangeable with Fred and George Weasley, who also go on to use the Marauder's Map (invented by James and Sirius and their friends), as well as one of them dying and leaving the other scarred for life. If you changed the names in the 800-word prequel, the story would fit exactly to Fred and George with the exception of physical descriptions, their dialogue has exactly the same patterns and brand of humour, making James and Sirius seem very shallow in development (at least, them in their youth.)
Many of the characters were inspired by either other fictional characters or people in real life. For example, Harry and Dumbledore are expies of Wart and Merlin from The Sword In The Stone, Hermione is an Author Avatar, Aunt Marge and Dolores Umbridge are expies of Margaret Thatcher, and the Big Bad himself is an expy of Adolf Hitler and Darth Vader/Sidious.
In the first book, there's a member of Dudley's gang named Piers Polkiss. From his description and what little we see of his personality, he's essentially an early version of Peter Pettigrew.
David Eddings does this repeatedly, blatantly, and unashamedly... so blatantly, in fact, that it becomes a plot point, at least in-universe.
If you click on Robert A. Heinlein you will see listed on his page his three most common character types.
Technically, mystery writer Dick Francis didn't reuse protagonists, but in terms of personality, they're all exactly the same guy.
Yes, he did. Sid Halley (4 books) and Kit Fielding (2). How sad is it that I know this? But otherwise, yeah, they're all pretty much the same bloke.
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.
Given what's known about Jim Butcher's love of comics, Harry Dresden of The Dresden Files can be seen as an Expy of Spider-Man, with magic instead of radioactivity.
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.
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."
Oscar Wilde did this - the briefly-mentioned Baron von Arnheim (aristocratic, art-loving, corrupt, heavily implied to be gay) in An Ideal Husband is an obvious expy of the (ditto all of the above) Lord Henry in The Picture of Dorian Gray. Lord Illingworth from A Woman of No Importance differs from the other two only in being slightly less evil and slightly more attracted to women.
In the Beauty Trilogy, by Anne Rice, the character of Laurent is exactly the same as Lestat, minus the vampirism.
Margo of John Green's Paper Towns is essentially Alaska of Looking for Alaska. Though Margo is toned down from manic Alaska, the two have a similar purpose, the unreachable and mysterious object of affection for Q and Pudge (who are very similar and are largely considered author stand-ins).
Jane and her niece Eliza in Edward Eager's books.
Several of William Makepeace Thackeray's novels have female characters with a B. name who are The Vamp or a Femme Fatale (Becky Sharp in Vanity Fair, Beatriz in Henry Esmond, and a Blanche in Pendennis).
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.
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.
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.
Percy Jackson and the Olympians has Connor and Travis Stoll, who while not actually twins (Connor is a year older) are pretty much the Weasley Twins without the red hair and large family, and with an added streak of kleptomania.
We also get some of this with the main characters - Percy seems to be an expy of Harry Potter himself, which would make Annabeth Hermione and Grover Ron. (so... Rick Riordan was a Harmonian?)
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.
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 Immortal Soul... it's all there, just dressed up with more tentacles.
However, it's been pointed out that The Dream-Quest of Unknown Kadath can be read as A Princess of Mars with Eldritch Abomination horror.
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.
Stock characters are pretty much the same across several of V. C. Andrews' series. The heroines, their love interests and their children seem to follow the same kind of mold, with a few deviations. So do the "evil grandmother" figures (Olivia Foxworth, Olivia Logan, Lillian Cutler ...), the "jealous sister" figures (Vera Whitefern, Fanny Casteel, Clara Sue Cutler, Allison Randolph ...), the "vain mother who doesn't care" (Corrine Dollanganger, Jillian Tatterton, Laura Sue Cutler, Haille Logan, Megan Hudson ...) and the "perverted old men" (Tony Tatterton, Octavius Tate, etc).
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 Warhammer40000. 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.
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).
It might border on Captain Ersatz, given the similarity of names, but in A Song of Ice and Fire, Samwell Tarly is an affectionate Shout Out to Samwise Gamgee of Lord of the Rings, and with this in mind, it also seems like Those Two Guys on the Night Watch, Grenn and Pyp, are supposed to suggest Merry and Pippin.
In Alice's Adventures in Wonderland, Alice meets the Mad Hatter and the March Hare. In Through the Looking Glass, she meets two of the White King's messengers, Hatta and Haigha (Hatter and Hare).
The novel Memoirs of a Teenage Amnesiac features a character who closely resembles Ducky from Pretty In Pink, in his flamboyance, his status as the female protagonist's "best friend", and his Everyone Can See It crush on her. Unlike Ducky, he gets together with the protagonist in the end.
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).
Noel Streatfeild often does this with a character who is a nanny or nurse to the protagonist(s). Hannah in Thursday's 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.
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.
Intra-universe example: Terry Brooks' 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.)
Fifty Shades of Grey is an outrageously popular erotic novel trilogy that started as a Twilight fanfic. A fascinating breakdown of the similarities between the original fanfic and the published novel is here.
In the Infernal Devices series, the heroine, Tessa is a blatant Expy of the heroine of Cassandra Clare's previous series, The Mortal Instruments. Not to stop there, the love interest, Will, is the exact same character as the hero of the first series, Jace; the third member of the Power Trio, Jem, is a combination of Simon and Alec,
He used a Force Choke on an officer that had failed him.
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.
Academ's Fury, second book Jim Butcher's Codex Alera features the Vord. 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.
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.
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.
In the book Fat Kid Rules The World, the protagonist's friend is a punk rock guitar god named Curt Maccrae. Sounds familiar.
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.
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 Eleventh Hour Superpower. The key difference between them is Benji doesn't say Shout Outs to real world products.
The protagonists of The Host, Wanderer and Melanie, seemed to remind me of someone from another book Meyer has written recently... I just can't put my finger on it. Granted, they both have a lot of differences too, mainly that Melanie's a bit of a Tomboy with basic survival skills that Bella lacks. And Wanderer, well, Wanderer's an alien.
Also, the Souls themselves, who are a rehash of a very old idea*
