The episode "Where No Fan Has Gone Before," having united almost all the Star Trek original cast, gave us a Suspiciously Similar Substitute named "Welshy" who apparently replaced James Doohan for a musical reunion in the 22nd century. This was almost certainly a pointed comment on Doohan's refusal to participate, since the late DeForrest Kelley was just The Voiceless and Welshy was quickly killed off. This was lampshaded in the episode's working title — "We Got Everybody But Scotty."
Lampshaded in the episode "Godfellas" with Helper, a Bender replacement that makes wacky noises.
In "When Aliens Attack", Professor Farnsworth assumes Fry, Leela and Bender have died in the latest mission, prompting him to hire a nigh-identical trio.
Farnsworth:[to the near-Leela, -Fry and -Bender duplicates respectively] You'll be the captain, you'll be the delivery boy, and you'll be the alcoholic, foul-mouthed... [notices regular crew standing in the doorway] Oh God, you're alive! [to the near-duplicates] Sorry about this. Check back in two weeks... a month, tops.
Darby replacing Christopher Robin in My Friends Tigger and Pooh.
Though Christopher Robin does appear a few times in the later episodes.
Lady Jaye and Scarlett are interchangeable, despite being written as very different characters in the Marvel comic.
Duke from the Sunbow series was essentially a carbon copy of Hawk from the Marvel comics, who was the originally established blond-haired leader of G.I. Joe. This change was done since at the time the animated series started, Hasbro was phasing out the original 1982 lineup and wanted to promote the newer figures being released in 1983, from which Duke was part of. Duke's character design even resembled the way Hawk was depicted in Sunbow's original TV ads for the G.I. Joe toys and comics (see here). When a second Hawk action figure was released in 1986, he was introduced to the animated series during the year's season as Duke's heretofore unseen commanding officer, getting an Adaptation Dye-Job in the process from blond to black hair.
When Hasbro relaunched the G.I. Joe toyline in 2001, they wanted to bring back Roadblock into the lineup, but couldn't due to trademark issues with the character's name. So Heavy Duty, an already-existing separate character, was made into a virtual Roadblock clone. The Spy Troops CG animated series tried to explain away their similarities by claiming they were cousins.
The octopus replacing the crocodile in Return to Neverland. It inexplicably starts ticking after it decides to eat Captain Hook.
King Larry replacing King Louie in House of Mouse. This was due to legal action when Gia Maione, the wife of original actor and now deceased entertainer Louis Prima, sued Disney for unauthorized use of her husband's persona because voice actor Jim Cummings' impression (as heard in TaleSpin) was too dead on. Part of the out of court settlement is that Disney could no longer use King Louie.
Though the character existed before, Gil took Lionel Hutz's job as the family's lawyer after Phil Hartman died.
This trope is parodied in "Donnie Fatso", in which Fat Tony is replaced by his nearly identical cousin Fit Tony, who gains weight and is eventually called Fat Tony.
In the DVD commentary to "Alone Again, Natura-Diddily", some of the writers joke that since they miss Maude Flanders, they should write an episode in which Ned gets remarried to a woman that looks and sounds just like Maude. In the 22nd-season finale, Ned begins dating and by the next season has married Edna Krabappel.
In "A Star Is Burns", C. Montgomery Burns hires Steven Spielberg's "nonunion Mexican equivalent", Señor Spielbergo, to direct the fictionalized biopic A Burns for All Seasons.
In "The Saga of Carl", Homer, Lenny, and Moe try to find a replacement for Carl after he leaves the country. Initially they try putting Lou the Cop in the role, but he storms out when he realizes all they're looking for is a new Token Black guy.
After Kenny died "for reals this time", his spot as the fourth friend was filled by former minor character Butters. This is lampshaded as the other boys attempt to manipulate him by telling him that "Kenny would do" whatever crazy scheme they have in mind that week, going so far as to call him "Not-Kenny" when he resists. Butters is eventually "fired" as the fourth friend and the boys actually hold try-outs to fill the position. It is briefly filled by Tweek until Kenny eventually shows up (sans explanation) to reclaim his old spot. Indeed, he merely walks up to the boys from just offscreen, and announces that he was "hanging out", just after the boys have returned from Iraq after trying to give it Christmas.
Unlike most other un-substituted SSS's, Butters also managed to maintain an increased presence on the show, becoming somewhat of a Mauve Shirt.
The ever-Genre Savvy show also lampshaded this with Chef's temporary replacement Mr. Derp in the episode "Succubus."
This could easily be considered a reverse example, as Chromastone was something of this or an expy for Diamondhead in the first place.
A recent episode brought back Chromastone and revealed his connection to the alien race Diamondhead comes from.
Ultimate Alien introduces Fasttrack, who shares the exact same coloration and powers as XLR8, which is rather peculiar, as his existence could be considered redundant and unnecessary, considering Ben likely has XLR8 in his Ultimatrix, as almost every alien he's had in the previous two series is unlocked. Though he seems to be somewhat stronger and Matt Wayne did say that Fasttrack is stronger. XLR8, however, sees use in the Man of Action Studios-helmed Heroes United Crossover with Generator Rex.
Though the mentality behind making another very fast character (and similar substitutes in general) could be accepted if one were to consider the idea that of the million aliens connected to the Ultimatrix, it's highly likely that several of them naturally have the same powers. This circles back to why sets of 10 were created. Variety without redundancy.
In Mickey's Twice Upon a Christmas, Max's girlfriend Mona is a semi-Jonas Quinn of Roxanne from A Goofy Movie; she's actually voiced by the same VA, Kellie Martin. The plot at hand is that he's bringing his girlfriend from college home for Christmas to meet his dad. Roxanne obviously met Goofy before, so they came up with a new, suspiciously similar girlfriend character. (And, to be realistic, how many of you were still with your high school crush/sweetheart in college?)
Dawn is one to Bridgette, as both are pacifist nature lovers who were the first to be voted off by the season's big bad, thereby establishing Alejandro's and Scott's threatening natures.
Jo is one to Eva, as both are jock-ettes; hoever, she takes the general premise of Eva's character (brawn and a serious attitude) and builds a much more complex and hyper-competent competitor than her.
Scott is one to Alejandro and Heather as they are all arrogant, manipulative antagonists, who feign friendship in order to get ahead. Like Heather, Scott is bad at hiding his true nature, becomes a Butt Monkey as time passes, and eventually gets a Hispanic love interest. Like Alejandro, he gets severely injured towards the end of the season and is put into a mechanical suit to recover.
Zoey is one to Beth, as both are nice but socially awkward girls. However she later becomes closer to Bridgette.
Cameron is one to Harold, being the resident intellectual character, as well as to Cody, being the physically weak character. This is further affirmed in All-Stars, where Sierra literally sees Cameron as Cody.
Shawn is one to Ezekiel, as both are toque-wearing homeschooled boys.
Topher is one to Sierra, as both admire Chris McLean.
Ella is one to Dawn, as both are Nice Girls, are kind to everyone, have an affinity with nature, and have befriended many animals.
Taylor to Heather and Amy (all fall into the spoilt-brat group)
Miles to Bridgette (both calm girls who care about nature)
Devin to Trent (both kind and caring and can be oblivious to love)
In the 1980s, there was an animated Public Service Announcement featuring the Teen Titans. Since the producers didn't have the animation rights to Robin, they swapped him out for an extremely similar teen hero named the Protector.
In DuckTales, Launchpad McQuack and later Fenton Crackshell both acted in the role Donald Duck had from the original Uncle Scrooge comics, namely being the other adult character working with Scrooge and the nephews. The writers of the show were worried that Donald's presence would outshine Scrooge and the nephews, which was why the two other characters were created and so they would serve as the fifth member of the Five-Man Band in the first and second seasons. However, Donald did notably have a minor recurring role in the first season, where he would properly retake his position from the comics in the few episodes he appeared in.
A lot of the characters from My Little Pony: Friendship Is Magic were meant to be characters from previous incarnations of the franchise, but had to be changed due to Hasbro's trademarks for said characters expiring.
Starlight Glimmer, the Big Bad of season 5, is one for the spinoff-exclusive character Sunset Shimmer. Over the course of the fifth season, she's had the same arc as Sunset did in the first movie, and by all appearances will continue to develop on Sunset's path.
In an odd twist, Starlight Glimmer can also be considered a substitute for the original Unicorn Twilight from Seasons 1-3. The similar name, similar design, the Super OCD tendencies in her personality, the lack of social background and naivete, and the immense magical potential and ability that leads to her becoming being taken in as a student in the study of Friendship by an Alicorn Princess, just like Twilight originally was. She even sounds similar to Twilight in her voice and mannerism post Heel-Face Turn.
Korra's Mako for Avatar's Zuko, as the brooding, troubled firebender who has a tendency to get embroiled in shipping wars.
And Korra's Bolin for Avatar's Sokka, as the wisecracking, sarcastic and somewhat bumbling comic relief. They both even have a similar inferiority-complex arc in their respective third seasons, Sokka because he's a Badass Normal in a group of super-powered kung-fu wizards (until he finds a mentor and gains skill in swordsmanship), Bolin because he is only a "normal" Earthbender without a specialization like Mako's lightning-bending or Toph's metal-bending (until he learns how to lavabend).
Speaking of Avatar: The Last Airbender, Admiral Zhao died at the end of the Book 1 finale and gets replaced with Princess Azula, who is sent to drop the hammer and finish her predecessor's job.
SheZow had a sickly version of the main character, thus getting Kelly (his big sister) to become the superhero(ine) for a day (a la Freaky Friday).
Brittany from Alvin and the Chipmunks is one of these. A year prior to her and her sisters appearing, a solo Chipette named Charlene appeared in an album called The Chipmunks Go Hollywood. She had a blonde ponytail and was Alvin's love interest. A year later the other two Chipettes were introduced alongside Brittany, with Charlene being replaced. The main difference between the two is that Charlene had lighter hair and a black nose.