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Jessica Jones from Alias is an admitted expy of Jessica Drew. Alias was initially supposed to star Drew (hence the reason both characters are washed up former superheroes who become private detectives) before the Darker and Edgier nature of the series caused Marvel to request that Bendis use a new character instead.
DC's All-Star Squadron featured the Young All-Stars, who were meant to replace the Golden Age versions of Superman (Iron Munro), Wonder Woman (The Fury), Batman (Flying Fox), Aquaman (Neptune Perkins, Tsunami), and Green Arrow (Tigress) Post-Crisis, because they, you know, weren't active back then anymore. Neptune Perkins was a very obscure pre-existing character, for what it's worth. They had Nazi-created evil counterparts called Axis Amerika to contend with, which were also retrofitted Expies of the vanished Earth-2 heroes: Ubermensch (Superman), Gudra the Valkyrie (Wonder Woman), Grösshorn Eule and Fledermaus (Batman ), Usil (Green Arrow) and Sea Wolf (Aquaman). Part of the reasoning was that, metaphysically speaking, iconic characters like Superman and Wonder Woman were "too big" to be replaced by just one new (and inevitably "lesser") character. The Token Japanese member of Axis Amerika, Kamikaze was an expy of Fawcett's Bulletman.
Archie Comics even had its own Expies of Archie, including That Wilkin Boy and Wilbur.
Fast Willie Jackson was an African-American Archie Expy from Fitzgerald Publishing.
Atlas/Seaboard comics published Vicki circa 1975... a feature that itself consisted of slightly-updated reprints of another Archie expy, Tippy Teen, which had been published by Tower Comics in the '60s.
Archie is also an Expy himself, being heavily-based off of Andy Hardy, a popular character played by Mickey Rooney at the time.
The Colleen Coover character Bandette was inspired by the French costumed heroine Fantômette.
Kirk "Man-Bat" Langstrom is to Curt "The Lizard" Connors. Really, regardless of where each character ended up, the only difference between their origins is the specific ailment they were trying to cure and the specific animal they were working on.
Number 13, a strip about a supernatural family of monsters in the Anthology ComicThe Beano was The Munsters. Also Kat and Kanary is Sylvester and Tweety from Looney Tunes. The character Joe Jitsu from the 00s seems to be an expy of an earlier character entitled Karate Sid from the 80s.
In the Catwoman story "Selina's Big Score", Stark is a blatant Expy of Parker, Villain Protagonist of a series of crime novels by Richard Stark. He also looks like Lee Marvin, who played Parker (renamed Walker) in the film adaptation of the first novel, Point Blank. (Darwyn Cooke, who wrote and drew the story, later went on to officially adapt the Parker novels to the comic medium.)
The Crimson Avenger and his sidekick Wing started off as thinly-veiled Expies of The Green Hornet and Kato, but then evolved into Expies of Batman and Robin after superheroes started becoming more popular.
Diabolik had a major series of expies. Interestingly, these expies lost their readers and ended publication by staying true to Diabolik's initial noir while Diabolik and the only surviving expy (Paperinik) moved to other genres (Diabolik to crime fiction and Paperinik to superhero).
Marvel Comics' Donyell Taylor, originally codenamed Bandit, is an Expy of Marvel's own Gambit, a fact exploited shamelessly by an issue of Gambit's eponymous series when Bandit turns out to be romantically involved with Gambit's ex-wife Belladonna.
Lee, the main character of Peter David's Fallen Angel is an Expy of Linda Danvers, protagonist of David's previous run on Supergirl. In fact, David did his best to fuel speculation that the characters were one and the same until the book's second volume, in which he chronicled Lee's origins. Later on, he introduced Lin, yet another expy of Linda Danvers, who can in fact be considered Linda in everything but name. Likewise, the God figure in the series is a small girl dressed in a tennis motif and carrying a tennis racket, which makes her an expy of Wally, the god figure in David's Supergirl who was a young boy who carried a baseball bat.
John Byrne's college newspaper strip Gay Guy! had a villain called Charisma, whom no man could resist except... well, guess. Byrne liked the character concept so much that Karisma showed up on the Fantastic Four's doorstep a decade and a half later.
Ghost Rider villain Skinbender is plainly designed to heavily resemble Sailor Venus; true to this inspiration, she falls in love with Ghost Rider when they meet.
In the Godzilla (2014) tie-in Godzilla Awakening, Shinomura's design and abilities uses elements of Deathla (an unused Kaiju), Hedorah, and Destoroyah and a little bit of Ygramel the Many.
During the Golden Age, Green Arrow was given many similarities to Batman, right down to the Arrow-Car, Arrow-Cave, and a teen sidekick in Speedy (who is really just like Robin only a junky).
In a rather unusual example, in Marvel's Incredible Hercules and later, in Incredible Hulks, Zeus served as an expy for God. That is, the Judaeo-Christian God. Zeus, previously portrayed as distinctly unimpressive, especially next to his intelligent and scheming wife, became considerably more imperious - and when put on trial, threw the "angry at God" argument back into the faces of his accusers. When the Hulk confronted Zeus, the context was somewhat awkward if Zeus is taken as himself, but perfectly logical when read as God.
Mocked by Zeus himself. Hulk's reason for confronting him was that he wanted Zeus to help his family. As Zeus comments: "Offering yourself as a sacrifice. Dying for other people's sins. Wrong religion." bitchslaps
Invincible is full of them, mostly minor background characters but a few have been important recurring characters. The title character's father Omni-Man starts out as an Expy of Superman (but 10 issues in, his plot becomes Beware the Superman). The original Global Guardians team were all Expies of the Justice League until they were killed by Omni-Man and a more original team took over. Expies of Aquaman, Martian Manhunter, and Robin remained important supporting characters longer than the rest. Cecil is Nick Fury but just barely managed to keep his eye.
Ragged Robin of The Invisibles, is similar to Crazy Jane from Grant Morrison's Crazy Jane from his run on Doom Patrol. According to Morrison himself, they're the same person in a different universe. More of this on The Other Wiki. Alhough Ragged Robin does diverge from Crazy Jane and he invented a completely new Backstory for her.
There was one issue of Justice League of America written in 2000 by Greg Weisman, in which the League travels to Paris and meets a clan of gargoyles living in Notre Dame cathedral, all of whom are clear Expies of the main cast of Weisman's cult classic TV show Gargoyles. There's the leader, "Behemoth" (Goliath), his ex-lover "Diabolique" (Demona), his daughter "Angelique" (Angela), his second-in-command "Montmarte" (Brooklyn), Angelique's lover "Montparnasse" (Broadway), the diminutive smart guy "Champs-Élysées" (Lexington), the team mentor "Seine" (Hudson), the Team Pet "Left Bank" (Bronx), and Behemoth's Evil Twin "Thomeheb" (Thailog).
When the teen supervillain Kid Karnevil attempted to infiltrate the Justice Society of America, he did so by posing as a patriotic superhero named the All-American Kid. All-American Kid's costume and backstory were extremely similar to those of Bucky, the sidekick of Captain America.
Big Daddy from Kick-Ass is basically The Punisher with a badass little girl sidekick, Lampshaded when Dave compares him to Frank Castle. He and Hit-Girl are also similar to Cassandra Cain and her father in that, in spite of being trained to be a killer by him, still loves him.
Maximum Press characters Law and Order bear a strong resemblance to Marvel's Cloak & Dagger.
One story in The Maze Agency featured a detective named Senor Lobo, whom writer Mike Barr has acknowledged was a deliberate homage to Hercule Poirot.
For The Multiversity, Grant Morrison designed an Aboriginal version of The Mighty Thor called the Thunderer. This character and his group seem to be a nod to Mike Friedrich's Wandjina and the Champions of Angor, pastiches of Marvel Comics' Avengers. They get something of an updated appearance as "The Retaliators" when President Superman and the team arrive on Earth-8, one dimension shy of Thunderer's homeworld of Earth-7, indicating this world is connected to it in some way. The Fantastic Four and Dr. Doom receive similar treatment, becoming Earth-8's Future Family and Lord Havok respectively.
The Just #1 confirms that the relationship of Earth-7 to Earth-8 mirrors that of the Ultimate Marvel universe to the main Marvel universe, with Earth-7's versions being known as the "Essential" versions.
Pat Mills's The Punisher 2099 seemed a bit similar to Judge Dredd, an earlier character co-created by Mills, when he was introduced. When he was put in charge of the Punishment Police, this identification became certain.
Queen And Country is, as writer Greg Rucka fully acknowledges, heavily influenced by The Sandbaggers. Not every character is an Expy, but Paul Crocker and Tom Wallace are especially obvious as expies of Neil Burnside and Willie Caine, respectively.
Marvel/Star Comics' Royal Roy was basically an Expy of Harvey Comics' Richie Rich, back when the latter company wasn't publishing any books in the early 1980s. It was even handled by the same artist/writer team that created Richie Rich.
When Jack Kirby and Joe Simon took over DC's Sandman book, they immediately made him more like their old assignment (Captain America), right down to giving him an Expy of Bucky in "Sandy the Golden Boy."
Not too long ago, during Marvel's Dark Reign event, the "Sinister Spider-Man" title (Mac Gargan's Venom posing as Spider-Man) introduced us to Doctor Everything, a pretty blatant expy of Watchmen's Dr. Manhattan, right down to his....disturbing penchantfor nudity.
In a probably deliberate example, since the character is a Redeeming Replacement for one of Spider-Man's worst enemies, Phil Urich the heroic Green Goblin is an expy of Peter Parker. Urich is an Unlucky Everydude who works for the Daily Bugle and has an Uncle Ben just like Peter (although Urich's doesn't get killed). In the Spider-Girl series, the two characters are close friends.
Superman has so many expies flying around it could almost be a trope unto itself: Captain Marvel, Icon, Hyperion, Gladiator, Supreme, Virtue, Omni-Man, The Sentry, Blue Marvel, the Homelander, the Plutonian... and that's not nearly all.
When Alan Moore began work on Watchmen, the plan was to use all of the characters DC purchased from Charlton Comics, but editors ultimately put the kibosh on that, so he had to create new ones.
Hollis Mason/the first Nite Owl is an expy of the first Blue Beetle, Dan Garrett.
Dan Dreiberg/the second Nite Owl is an expy of the second Blue Beetle, Ted Kord.
And if it wasn't explicit enough, the later New Mangaverse series redesigned the Human Torch so that she looked even more like Asuka.
Happened all the way back during the creation of the X-Men by Stan "The Man" Lee himself. When creating the original team of five, Lee decided he wanted to re-use the character of the Human Torch, but with ice powers instead of fire. The youngest member of the team, and also the most irresponsible and hot-headed, with the opposite super power...
In recent X-Men comics, Hellion has become an Expy of Quentin "Kid Omega" Quire; Both have very powerful psychic abilities and inflammatory personalities to begin with, but Hellion's adopted Quentin's signature striped sweater-vest and started hanging out with Glob Herman, one of Quentin's old flunkies (and the only living member of the Omega Gang to still have his mutant powers). He's also spouting mutant supremacist rhetoric and telling baseline humans to "get back to your caves, apemen!"
Ironically, while this has been going on, Quentin himself has been moving into a more heroic role as a member of the X-Men proper.
There's also Onyxx and Rockslide, two X-Men who have roughly the same powers (being giant rock men) and only a few strong physical differences (different colors, Onyxx has a helmet and is slightly bulkier, slightly different costumes). It's to the point that, seeing them on the same page, you could think one was an artist/colorist error meant to represent the other. This is lampshaded a few times when they're shown to be casual acquaintances who think highly of one another.
Both happen to also look like a Palette Swap of The Thing, who almost certainly inspired their creation. The only difference power-wise is that Rockslide can fire off body parts; Onyxx and the Thing can't.
Abigail Brand's Lovable Rogue half-brother Lothi in the S.W.O.R.D spin-off has major similarities of appearance and personality to Tank Girl's boyfriend Booga. About the only difference is that he's green.
Riptide's father Storybook Smith is based off the Golden Age hero Johnny Thunder.
British comics examples:
During the 1970's and 1980's, IPC Magazines would often copy characters from DC Thomson's humour comics. Examples include 'Soldier Spoon' (a Corporal Clott expy), and 'Tricky Dicky' (a Roger the Dodger expy.) It may be worth noting that DC Thomson later made their own character called Tricky Dicky, who was similar to 'Joker' from IPC's Whizzer and Chips.
During the late 1980s and early 1990s, The Dandy made expies of some of IPC's characters, particularly those from Whizzer and Chips. An example of this is 'King Dom- the Dandy lion', who was an expy of IPC's own 'King of the Jungle', as well as an annual-only strip called 'Parental Pests' featuring a cast of characters who were shameless clones of those from IPC's 'The Big Kidds'.
An example from the same publisher was Challenge Charlie from IPC's Valiant which was an expy of the earlier Dare-a-Day Davy from Odham's Pow! (Odhams was taken over by IPC). Both strips were drawn by Ken Reid and on a few occassions the same scripts were used which lead to a couple of Challenge Charlie comic strips which looked suspiciously similiar to earlier Dare-a-Day Davy comic strips.
An oft-mocked facet of early Image Comics was that every team seemed to have a Wolverine expy, who had blades on his hands, a bad attitude, and a mysterious past. And while it wasn't every team (Gen 13 and Stormwatch being the most notable exceptions), this was true for most of them — Youngblood had both Cougar and Troll, Youngblood's "training squad" Bloodpool had Wylder, Cyberforce had Ripclaw, WildC.A.T.s had Warblade, Bloodstrike had Deadlock, and Codename: Strykeforce had Killrazor. Deadlock was probably the most obvious (and that's really saying something), since his first costume featured a mask nearly identical to Wolverine's.
Interestingly, Ripclaw, Warblade, and Deadlock are still appearing in comics as of February 2013, but have very little in common with Wolverine; Ripclaw's powers have changed from "clawed hands" to "shooting spikes", Warblade is a sadistic villain, and Deadlock is a Legacy Character with a more unique costume, Invisibility powers, and despite remaining a Sociopathic Hero, a much more stable personality.
Rob Liefeld is infamous for those. During his run on New Mutants and X-Force, he created Thornn and Feral- Wolfsbane Expys, Kane- A Cable Expy (which he also created) but younger, and Copycat- a Mystique Expy. Many many of his Image Comics characters are blatantly ripping off various Marvel characters as well, including ones he himself created.
He's even admitted that Youngblood was simply a rejected Teen Titans pitch, right down to the redheaded archer Shaft being Speedy/Arsenal and Diehard being a S.T.A.R. Labs android.
The New 52 character Niko was initially stated to be Cheshire in solicits for Grifter. This apparently changed before the issue hit stands, resulting in the character having a different backstory while still retaining a similar costume and appearance to Cheshire.
S.P.I.C.E. from his Fighting American run is a clear expy of Rikki Barnes from his earlier Captain America run, right down to having an extremely similar jacket and set of goggles.
The Fighting American himself was an expy of Captain America, though he dates back to the 1950's and was created by Jack Kirby.
Oddly enough, he received his own expy in the form of the Fighting Yank during his AC Comics series. The Fighting Yank was redesigned and given a costume almost identical to that of the Fighting American.
Even more oddly, Captain America himself is an Expy of a now obscure character, The Shield, also developed by Jack Kirby, and Joe Simon.
The 2099 incarnation of the X-Men has a lot of members who are clearly evocative of some member of the original team. The most obvious are Xi'an (the paternal mentor figure ala Professor X), Skullfire (the leader with energy blasting powers and Power Incontinence, like Cyclops) and Bloodhawk (the mysterious, brooding loner with anger issues and claws, as in Wolverine).
Detective Martin Soap, the comically unlucky cop from Garth Ennis's pre-MAX work on The Punisher, is an Expy for Detective Paul Bridges, a minor character from an early arc of Preacher.
DC's Bumblebee is an obvious Expy of Marvels' Wasp. Everything from the power set, to her costume to the double-banger name (Janet Van-Dyne vs. Karen Beecher-Duncan).