Atlee (aka Terra) after the writer/artist switch during Power Girl's solo series. She appeared in one panel of the first issue after the switch and was then never seen again. Especially noticeable as she had basically been Peeg's sidekick and was well liked by fans.
King Muskar XII of the fictional Balkan kingdom Syldavia was a major character in the Tintin story Tintin King Ottokars Sceptre (written in 1938), and ends up a close ally of Tintin. Yet he is completely absent for the post war stories dealing with Syldavia - in fact it is even unclear whether Syldavia is still a monarchy. Possibly a case of Reality Subtext: Muskar was based on King Leopold III of Belgium, who was forced to abdicate after World War II, and almost every Balkan kingdom except Greece was replaced by a republican form of government; although unlike the real-world Balkan states Syldavia did not become communist.
Surprisingly effective bad guy Doctor Strange easily defeated Iron Man and made a successful getaway when his too-honest daughter freed the hero. And he was never seen again! The name was later applied to Steve Ditko's unrelated magician. An explanation of what happened to him is long overdue by Marvel.
Famously done to Rikki in the Belgian comic epic Suske en Wiske (Spike And Suzy). Rikki was Wiske's brother, and a main character for the singular issue the comic was still called "Rikki En Wiske". He was never heard from again until after the author passed away, and the new writers decided to bring him back briefly after 254 (!) issues. The explanation? Rikki had gone out to buy shoes and somehow got stuck in Ruritania.
What exactly happened to Toxin in Marvel Comics is a topic that will likely never be resolved; even guys like Gravity and Sleepwalker get cameos now and then, but Toxin has plainly been abandoned entirely.
Toxin isn't the first symbiote character to disappear either, joining fellow heroic symbiote Hybrid and the female symbiote Donna/Scream.
In the current Venom series, the Toxin symbiote has a new host and is a villain now. Patrick Mulligan, its original host, died off panel. Hybrid and Scream were also killed off in this series.
In current Super Hero comics every time that either writer or status quo changes, most of the supporting cast and villains with exception of Ensemble Darkhorses (and sometimes even them) are put at risk of suffering from thiis. If there's no place for them in the hero's new life situation it can be justified. If they are gone because the writer didn't have an idea what to do with them, not so much.
When Brian Michael Bendis left Daredevil, the titular character had been imprisoned in one cell block with Kingpin, Owl and Jigsaw. New writer Ed Brubaker removed Jigsaw without any explanation.
Often happens to Spider-Man's supporting cast after all bigger changes of status quo.
Superman's post-Crisis supporting cast is notable because they were built up over such a long stretch of time, and then summarily jettisoned in 1999 when the Dan Jurgens/Louise Simonson era ended. Perry White's family, Bibbo and the other characters from Suicide Slum and the Bottle City characters introduced during the '90s all vanished abruptly never to return and characters like Emil Hamilton got thrust deep into the background overnight.
One of the most popular features of Bill Messner-Loebs' run on The Flash was the large supporting cast — they even carried the book without Wally for a couple of issues. When Mark Waid took over, all of these characters except Linda Park faded into the distant background. Piper showed up sometimes, and Chunk got the occasional cameo, but the new "Flash family" that Waid proceeded to assemble replaced everyone else (including Wally's real family). Waid's run was wildly successful, but longtime readers still regret the loss of those characters.
In the 90s, Lex Luthor was a prominent businessman who was ruthless but maintained occasional Pet the Dog moments. Among these was the fact that he had an infant daughter named Lena Luthor, who he loved very deeply but nonetheless got roped into his life as a supervillain against his wishes. After 2004 though, Luthor became a Mad Scientist for a little while and with Dan Didio and Geoff Johns at the helm of the DC, his character was sent into a different direction. In the midst it all, Lena just disappeared and it was never explained what happened to her or where she is now. At the moment, Lex Luthor's only biological child is Superboy.
Her disappearance was eventually explained. As a result of the Cosmic Retcons that took place during Infinite Crisis, Lena was Retconned into being Lex's younger sister (which she had been Pre-COIE) rather than his child. Lena's daughter Lori subsequently became a prominent supporting character in Superboy.
Happens with ridiculous regularity in the X-Men books, especially once Xavier's Institute became a full-fledged school with a student body beyond the active team members, only getting worse after the "Decimation" event reduced the mutant population to around 200 (prompting the X-Men to try to get literally every mutant on Earth to live at the X-Mansion and, later, Utopia). Whenever a new writer takes over, you can count on at least half the extended cast quietly vanishing. Sometimes a later writer will remember them and either mention where they got off to or reveal that they've been there all along never really doing anything.
Dana Drake, the stepmother of Tim Drake, the third Robin, is a particularly egregious example. When Tim's father Jack was killed off in Identity Crisis, it was done so Tim could be tied more closely to Bruce, who would formally adopt him. The problem is, though, that Jack had remarried to Dana, who'd been a major supporting character all through Robin's own series. Dana would have a mental breakdown over Jack's death and be sent to a sanitarium to recover... In Bludhaven, which would soon be completely destroyed in Infinite Crisis. One could assume Dana died along with everybody else in Bludhaven, but it was never explicitly stated she did. Instead, she has simply never been mentioned again. Evidently, DC editors wanted to get rid of her, but realized having Tim Angst over losing both his father and stepmother in 2 close together yet completely isolated incidents was too much even for DC. She'd be a Forgotten Fallen Friend except it was never confirmed she'd fallen. So instead, she's this trope.
The Impulse supporting cast soon vanished after his book ended, most notably Bart Allen's best friend Preston and love interest Carol. Much to fans' displeasure, one line in Geoff Johns' Teen Titans had Bart suggest it was Wonder Girl who got him to like girls, rather than mentioning Carol or even Arrowette (another crush of his). Bart's pet dog Dox was also never seen again or mentioned by any later writers.
Holly Robinson was one of Catwoman's prominent supporting cast members, even temporarily taking on the codename for an arc in the One Year Later era. However, after the "Countdown" event, Holly vanished and was never seen again in the Batman universe. A later throwaway line about the character suggests that she moved elsewhere after receiving a huge sum of stolen money from Hush's fortune. This is in no small part because of the sorry reputation her creator, Frank Miller, picked up over the years–the makers of The Dark Knight Rises even went so far as to create a similar character called Jen to avoid having to forward any money to Miller.
Post-CrisisWonder Woman's adoptive mother Julia Kapatelis. When George Perez was removed from the series, she vanished for some time. Her daughter Vanessa would also disappear, until she was retooled as a new Silver Swan.
This is pretty much true for most Wonder Woman characters not created by Perez or the original Golden Age creators. There are tons of love interests, supporting cast members and villains who simply never appeared again after their respective creator left the series. The few exceptions would be characters like Phillipus and Artemis, and even they seem to have been dropped as of the New 52 revamp.
A mid-story issue of the Super Mario Adventures comic strip, which ran in Nintendo Power during 1992, featured this. Toad uses a Cape Feather to fly up to a pipe sticking out of a cloud (allegedly the one Mario and Luigi entered at the beginning of the story to unknowingly wind up in Dinosaur Land), and gets "help" - which is actually Bowser's Koopa Troop in disguise (the cloud was actually an airship of sorts in disguise). After the Princess gets kidnapped, Toad is shown being held hostage by two Koopas, delivers one line about the Koopas "taking control of the Mushroom Kingdom", and is then never seen or mentioned again for the remainder of the comic (So they just left Toad in the Koopa Castle dungeons?).
In the Star Wars: Tales of the Jedi comics, main characters included Nomi and Vima Sunrider, the latter of which was going to be in Knights of the Old Republic. However, due to unclear trademark restrictions involving the name "Sunrider" (speculated to be from either a brand of convertible tops for Jeeps or some kind of corporation that makes herbal products, neither of which is very easy to mistake for a comic character), the characters stopped appearing at all in the Star Wars Expanded Universe, aside from an accidental anecdote in the first KOTOR game and an item description that didn't mention the last name in the second. However, Lucasfilm Licensing has apparently gotten past the worst of it, and can now create products and media featuring the characters, provided the name "Sunrider" isn't mentioned on the external packaging, and a book about Nomi Sunrider was due out in 2011. (See Wookiepedia.) For whatever reason, however, the book was cancelled.
Blackhawk: The early stories in the 1940s featured three squadron members named Zeg (Polish), Boris (Russian) and Baker (English). They all vanished without trace after their initial appearances.
Boris DID return briefly in the short-lived mid-1970s revival.
When the Micronauts began appearing starting in 1996 issues of Cable, not only was their reappearance due to a very apparent retcon, but no mention was made of Acroyear or Huntarr. Acroyear's absence is most likely due to the fact that Marvel no longer has the rights to any of the Micronaut characters derived from the old-school toyline. It doesn't explain why Huntarr is not there, as he was created by Marvel writer Bill Mantlo.
Wayne's in Pain, a character put into The Bash Street Kids (a comic strip in the Anthology ComicThe Beano) after a Blue Peter competition, disappeared after being in the strip for only a short while.
A number of characters from the Sonic the Hedgehog series have disappeared from the face of the Earth, especially if they weren't mainstream Sega-based characters or part of the Saturday Morning series. However, one bad example of this is Dulcy Dragon, a character from the second season of the Saturday Morning cartoon. She had a few roles up until issue 50 before appearing in a set of back stories along with Amy Rose. Beyond one last appearance in the early 100s, Dulcy has rarely, if ever, been seen again.
However, Ian Flynn's run has revived a number of characters and pulled them out of this hole, including Scratch, Grounder and Coconuts, and obscure, early issue characters such as Larry Lynx and Harvey Who.
On the other hand, thanks to a heaping dose of Screwed by the Lawyers, a large majority of the non-SEGA-approved characters (re: those created by former head writer Ken Penders) have disappeared due to Cosmic Retcon. However, being what the comic is, the entire thing is lampshaded greatly.
A side-effect of being such a Long Runner, Archie Comics have introduced several characters who never appeared after a few issues. Sometimes their absence is explainable, like the alien characters who have landed and vanished soon after. But then we have cases like Betty's older brother and sister, who have been recurring characters in Little Archie but are never mentioned in any of the teen or adult Archie stories.
Wiccan of the Young Avengers originally had two younger brothers, who have since fallen off the face of the earth.
Marvel Boy (formerly the Protector) had a girlfriend named Annie while he was a member of the Avengers. They had a very close relationship, and there were even some dangling plot threads concerning their relationship when Bendis left the book. Then came the second volume of Young Avengers, where Marvel Boy was shown shacking up with Kate Bishop without even a single mention of Annie.
This was eventually explained. Marvel Boy dumped Annie at some point between The Avengers and Young Avengers, leading to her eventual return as an Ax-CrazyWoman Scorned.
DC attempted to retool the Hawk and Dove concept in the late '90s with a book starring two winged humans; an army brat named Sasha, and a laid-back rock musician named Wiley. Due to the In Name Only nature of the characters and the lackluster reception, the two quickly vanished, not even to be brought out as cannon fodder in any events. For all intents and purposes, the two characters seemed to have never existed.
Despite the fact that Robotech: The Shadow Chronicles occurs partially during the same timeframe as final episode of the original Robotech series, Rand, Rook, Lunk, Annie, and Lancer are not seen or mentioned at any time. In the Prelude to Shadow Chronicles prequel, several Sentinels characters are not mentioned at all, such as Burak and Invid defector Tesla, leaving both of their storylines unresolved (although they were resolved in the original Jack Mc Kinney novelizations, they may have been retconned out given that Prelude presents a revised ending to The Sentinels).