In Captain America (vol. 1) #225, Steve Gerber created a new origin for Steve Rogers, revealing that he was from the Midwest and had an older brother who died at Pearl Harbor. The story was stricken from canonicity by later writers, with Gerber's origin handwaved away as false memories implanted by the government in case Steve was ever captured.
Captain America vol. 4 had a controversial story by John Ney Rieber and Chuck Austen, which implied that the story of how Cap had been frozen (recounted in The Avengers (vol. 1) #4) was a lie. "Ice", Austen's follow up story arc, revealed that the U.S. government had frozen Cap so that he couldn't prevent the atomic bombings of Hiroshima and Nagasaki, and that the Flashbacks from Avengers (vol. 1) #4 were Fake Memories. Austen was soon replaced, and the Retcon was never mentioned again.
The Conspiracy mini-series strongly implied that the rise of superhumans during the Silver Age was a deliberate conspiracy masterminded by a shadowy government cadre known as Control. This has never been mentioned again, and was later contradicted by the events shown in Matt Fraction's The Defenders run.
The Sensational She-Hulk #36 had Shulkie offhandedly remark that, since her graphic novel, Ceremony, was filled with errors about Wyatt Wingfoot's family, it "must've been a dream, or something".
One series written out of continuity was Spider-Man: Chapter One, which ineptly updated several bits of Spider-Man's origin; for instance, the Sandman and Norman Osborn were now related, as a way to explain their similar-looking hair. In a case of this being combined with Armed with Canon, John Byrne intended for this to overwrite Untold Tales of Spider-Man — only for Marvel to 1) tell Paul Jenkins to go with the classic Amazing Spider-Man for Webspinners: Tales of Spider-Man (which, given when it happened, meant Marvel wasn't even waiting for Chapter One to be finished before striking it from canon) and 2) continue to treat Untold Tales as canon, as its events would be mentioned and characters from it were seen again through later books.
Marvel's vague statements either took Trouble out of continuity or implied that it never was in continuity. This series depicted Peter's parents, along with Aunt May and Uncle Ben, as unwed teenagers and implied May was really his mother. Mark Millar ultimately tried to salvage Trouble as canonical in the last issue, trying to establish it as taking place in the Ultimate Marvel Universe via having reference be made to the Ultimate Marvel version of Bucky Barnes (who survived the war and became a famous writer). However, no one else has bothered to pick up on it and it's still a stand-alone story, mostly because it doesn't hold up to anyone with an understanding of basic math. Ultimate Avengers seemingly cleared up the issue by establishing that Trouble is simply a comic-within-a-comic in the Ultimate universe.
The reveal that Eddie Brock had cancer before bonding to the Venom symbiote, as well as an uncle who died of cancer, was disregarded by Venom: Dark Origin and retconned entirely by Donny Cates' Venom run, which revealed that the symbiote had been gaslighting Eddie by implanting memories of him having had a sister and uncle, and that Eddie himself had had cancer before bonding to it, in order to make him afraid to separate from it again.
The Venom symbiote is tricked into permanently bonding with Eddie Brock, angrily telling Spider-Man that he's doomed it and its unborn child. Both of these plot points were subsequently ignored, with Venom (Vol. 1) showing the two separating, Eddie later selling the symbiote to the Maggia on the black market, and the next significant symbiote spawning being Carnage's offspring Toxin.
Spider-Island brought back Adriana Soria, but ditched the "insect gene" plot point in favor of folding her into the Spider-Totem plot thread introduced by J. Michael Straczynski in his The Amazing Spider-Man (Vol. 2) run.
The entire premise of Sins Past was thrown out the window by Last Remains almost two decades later, with it being revealed that Norman's affair with Gwen was fabricated by Harry Osborn with Mysterio's help, and the Stacy twins were test-tube babies created via cloning by Harry and the Osborn AI as part of a complex posthumous revenge scheme.
During John Byrne's run on The Incredible Hulk (1968), an angry response to writer/artist, particularly his "Man of Steeling" of the Hulk in Annual #1, was responded to in the title's letters page by something along the lines of, "When you not like what happen, do what Hulk do: Pretend it never happened." Thus, the six issues and an annual were simply removed out of existence.
In Vol. 2, #269-287, the Rampaging Hulk stories were retconned into being techno-art movies by the Krylorian Bereet.
During Peter David's "Tempest Fugit" storyline, one line discontinuitized the entirety of previous writer Bruce Jones' 42-issue run.
A particularly brutal version happened in the first issue of the ClanDestine/X-Men mini-series. In one line of dialog, Alan Davis (ClanDestine's creator and artist/writer on the original Clan mini) rendered the entire second half of the original mini (i.e. The Issues He Didn't Write) as All Just a Dream.
New Avengers: Illuminati #3 completely redefined the nature of the Beyonder, the villain of the first Secret Wars (1984), as a mutant inhuman. It did not stick. Hickman introduced instead a whole race of Beyonders, with the one from Secret Wars being just a child one, and the events of New Avengers: Illuminati #3 being instead him trolling the members of the Illuminati.
Chuck Austen's X-Men run is treated as such outside of the Broad Strokes. Later writers have gone back and forth on his Avengers run, though. Bendis' Avengers Disassembled used Austen's plot point about Hawkeye sleeping with The Wasp and suddenly disliking Hank Pym as a key plot point (as a conversation about the Wasp's relationship with Hawkeye is what leads to Scarlet Witch accidentally remembering her babies), but Rick Remender's Secret Avengers run once again had Hawkeye and Pym as close friends, seemingly ignoring Austen's story.
Marvel declared certain issues of Ultimate Marvel Team-Up, including the Ultimate Spider-Man Super Special one-shot that closed it out to be non-canon. This was due to Early-Installment Weirdness in it that depicted the Fantastic Four and Doctor Doom much closer to their 616 selves (including having been active for a while, and Reed, Sue, Ben, and Doom very much being adults) rather than the rookies teens that Ultimate Fantastic Four introducted and, again, issues with Tony's origin.
The Ultimates: Tomorrow Men was a sequel to the first miniseries of The Ultimates in literary form. It continued the several plotlines left by it: Thor's real nature, the relation of Iron Man and Black Widow (and their "last sex before the apocalypse"), the relation of Captain America and the Wasp, the status of Henry Pym, the fate of the jailed Bruce Banner, etc. Mark Millar, the writer of the first miniseries, ignored all this and continued all those plotlines his own way in the second miniseries.
At one point in X-Men, the lineup at the time (Storm, Wolverine, Psylocke, Longshot, Dazzler, Colossus, Havok, and Rogue) were killed and resurrected, making them invisible to cameras, and this is treated almost as a second mutant power in the next few dozen issues. When Chris Claremont left, however, this was completely forgotten, and the lineup at the time are seen on camera without comment from then on. His run in 2000 makes a brief mention of this fact with Rogue, but this only serves to muddy the waters further — where it's been mentioned at all, it's explained as a side effect of the Siege Perilous, except that Wolverine and Longshot never went through it, and Rogue did. Common fan explanation is that Roma quietly revoked the "invisibility" gift around the time of the Xtinction Agenda crossover (which is where Claremont actively stopped referencing it) and that the gift itself may have been contingent on the X-Men both possessing and going through the Siege Perilous. Another possibility is in Excalibur when Meggan destroyed the Lighthouse, which was considered the "Lynchpin of the Multiverse", and its destruction may have disrupted Roma's powers. It happened shortly before Xtinction Agenda, which would explain the X-Men being able to be seen on television during the storyline and afterwards.
Marvel: The End was speculated to be in continuity. Tom Brevoort has stated it is not in continuity.
Nextwave is probably the oddest example of this trope ever made. Officially, it is not canonical, but most fans (and quite a few writers!) treats the act of making it discontinuity as a discontinuity in and by itself. This has caused some of the lunacy contained within the series (mainly the parts containing Machine Man and the other team members) to spill into the Marvel mainstream.
The Beyond Corporation from the series later reappeared in Mighty Avengers and Spider-Man Beyond. The official explanation is that the series is canonical, but took place in an alternate universe that Monica and the others had been kidnapped and sent to. Monica claims that once she got back to Earth-616, everyone around her assumed she was insane whenever she brought up the events of Nextwave.
Basically, what happened with Nextwave was that readers and creators agreed nigh-universally that the mad characterizations dreamed up by Warren Ellis were a zillion times better than their prior incarnations, so they've been bleeding into mainstream Marvel ever since. Elsa Bloodstone is now 100% Nextwave, and all the better for it. Monica Rambeau is probably the closest to a "split personality" situation. If she appears with straight hair and calling herself "Spectrum," then she's going to be a responsible cosmic-level Avenger, similar to her pre-Nextwave characterization. If she shows up with natural hair and wearing a trenchcoat, she's likely to call herself "Auntie Monica" and deliver oodles of snark and ultraviolence.
Secret Invasion ignored the X-Statix Presents: Dead Girl mini-series, where the Avengers member Mockingbird appeared in the afterlife. Invasion established that Mockingbird had never really died in the first place, making the series moot. However, the series' artist Nick Dragotta did later imply the events of the series were somehow still canonical when discussing the new Miss America he created for the Vengeance mini-series, making the Dead Girl's canonicity difficult to determine. It doesn't help that much later in X-Men (2019) that Moira MacTaggert was also revealed to be alive all this time, having faked her death with a Shi'ar golem.
Along those same lines, Brian Michael Bendis brought back The Wasp after killing her in Secret Invasion, with the explanation that she'd never really died in the first place. However, Wasp had earlier appeared in an issue of The Incredible Hercules where she was seen in the Greek Underworld, establishing that she was indeed dead. Though since the fandom was quite happy to have Jan back, there wasn't too much fuss.
Jeph Loeb and Daniel Way's critically-panned series Wolverine: Origins had the premise of exploring Wolverine's Mysterious Past, which by that point had already been quite fleshed out, so the series consisted of the writers inserting new, unknown elements of his history in among the existing stuff, making Wolverine's origin one huge Continuity Snarl. Among the "revelations" made were the fact that Wolverine is not a mutant after all but rather a "lupine," a species that looks completely human but is actually canine rather than primate in origin, and that Logan's mysterious, immortal ancestor, the founder of "lupine" society, had been behind basically every threat he'd ever faced, including the Weapon Plus program (even though the mastermind of that had already been revealed as someone else in a far better story). This was swept under the rug almost immediately after the run ended; whenever Logan's species has been referred to since then, he's always been called a human mutant, with the lupine thing revealed in the last parts of the run to be a lie, and the writer of a miniseries set during the same time period as Origins confirmed he'll be ignoring it, quite simply because it would be too confusing to acknowledge. Nothing from the run has ever been brought up again, with the exception of Daken, Wolverine's son, whose origin is heavily tied to all of the above... which writers thoroughly, thoroughly ignore and have never brought up again aside from vague references to Logan not being there to raise him and Daken having a cruel upbringing, with zero specifics as to what happened.
If a writer writes anything involving the Phoenix Force, it is bound to be rendered non-canonical by the next writer that writes something involving Phoenix. Most notably, Avengers vs. X-Men ignored the Alan Davis-penned Phoenix Force stories from his Excalibur run, which among other things established the Phoenix Force as Merlin's private energy reserve stash based off of the lifeblood of the universe, as well as establishing that any usage of the Phoenix Force is enough to bring the various cosmic forces down upon the wielder, as every time a user uses the Phoenix Force, the collective life force of the universe is drained.
Endsong, which was a sequel to The Dark Phoenix Saga, was declared non-canonical almost as soon as it was written. It was not until Avengers vs. X-Men that it was restored to canonicity, with Wolverine giving a vague recap of the story to the Avengers when discussing how the Phoenix Force possessed Jean's corpse and why Scott Summers was batshit insane to want to try and force Hope to bear its power.
Everything previously established about the White Queen (complete with her being in her 40s) was wiped out by the combination of Grant Morrison's New X-Men run and Emma Frost's short-lived flashback ongoing series.
The first arc of Reginald Hudlin's Black Panther wasn't meant to be canonical at first, which is why the book gave a radically reworked origin to Klaw (making him a Cyborg instead of a being of living sound), and then had him Killed Off for Real. Klaw has since shown up again in the Marvel Universe with his classic appearance and no references to his "death".
The Sensational She-Hulk started issue 31 (John Byrne's return to the series) by immediately establishing that everything that happened since issue 8 (the previous issue that Byrne had worked on) was All Just a Dream. (the cover even has Byrne trying to place an "Issue 9" sign over the actual issue number)
Ka-Zar: The Ka-Zar stories featured in these early comics are considered non-canon to both the later Ka-Zar series, and the Marvel Universe as a whole. The Golden Age Ka-Zar was called "David Rand" and was active in Africa, while the Silver Age (and still appearing) Ka-Zar was called "Kevin Plunder" and was active in the Savage Land, a fictional region of Antarctica. Besides the shared code name, they have little in common.
Garth Ennis has always asserted that Thor: Vikings is canon to Earth-616 (or "Mainline") Marvel, despite the fact it was printed under the usually explicitly non-canon Marvel MAX imprint. No authors have ever made any reference to the events of that story, outside of a single panel in a The Mighty Thor issue where one Viking disparagingly refers to "the goatfuckers of Harald Jaekelsson" (the mini-series' Big Bad). Whether this refusal is acknowledge it is due to the difficulty of having to work that story seeing New York City turned into a literal death camp, with tens of thousands of people either directly murdered, tortured and/or raped by undead Vikings or committing suicide as a result, into their own stories, or simply because fans universally despise the series is unknown.
either took Trouble out of continuity or implied that it never was in continuity. This series depicted Peter's parents, along with Aunt May and Uncle Ben, as unwed teenagers and implied May was really his mother. Mark Millar ultimately tried to salvage Trouble as canonical in the last issue, trying to establish it as taking place in the Ultimate Marvel Universe via having reference be made to the Ultimate Marvel version of Bucky Barnes (who survived the war and became a famous writer). However, no one else has bothered to pick up on it and it's still a stand-alone story, mostly because it doesn't hold up to anyone with an understanding of basic math. Ultimate Avengers seemingly cleared up the issue by establishing that Trouble is simply a comic-within-a-comic in the Ultimate universe.