Transformers Generation Two has become this. With IDW refusing to collect it and the UK exclusive TP Bs long out of print
Jerry Siegel and Joe Shuster produced the first full-length Superman comic in 1933, five years before his official debut in Action Comics #1. When the publisher pulled out, Shuster threw the whole thing in the fire out of frustration. The only part that survived was the cover◊.
Similarly, there was an issue of the Warren Ellis run of Hellblazer that was set to be published during the days when school shootings were the latest panic... and implied that some students, due to the rundown nature of modern life and teenage pressures, wanted to be shot. When Columbine occurred, that one hit the bin quickly. As of 2010, it's been pulled back out and published in a compilation book of lost and rare Hellblazer stories.
Many comics that feature licensed non-Marvel/DC Universe characters (For example, Marvel's Star Wars, Star Trek, Ren and Stimpy and Tiny Toons comics, and DC's own Star Trek comics) are not reissued most of the time due to licensing disputes with the character owners (these types of comics had licenses that had expired at a certain point in time; the publishers and/or artists still hold the comics' copyrights, but they do not own the characters themselves). Some may never be published again (So far, Marvel's Star Wars comics have not gotten a reissue by Marvel themselvesnote though Dark Horse (the current Star Wars license holder) DID eventually release the series in graphic novel format, and attempts to reissue Tiny Toons comics are blocked due to Marvel's rivalry with DC) unless the character owners reach a deal with the publishers.
Archie's Sonic the Hedgehog comics has been heavily compromised due to problems with a previous artist and writer, Ken Penders. His claims of copyright forced Archie to file a claim against him, which they eventually lost. The actual damage remains to be seen, but Archie went a head and wrote all characters created by Penders out of the book.
As of issue #252, the comic has undergone a soft reboot via Cosmic Retcon - the comic leans more heavily on the games than it did SatAM and the only people who remember the old universe are the main heroes and Dr. Eggman
Gotham Knights #12 was originally supposed to have an Elseworlds-style story by Devin Grayson about Mr. Zsasz killing Batman, but it was changed at the last minute after being deemed too graphic for an all-ages book. You can read about it here.
The Judge Dredd "Cursed Earth" epic had two arcs that, for legal reasons, could not be reprinted. EVER. One involved a war between McDonald's and Burger King, which had attained power greater than medium-sized countries. In the other, Dredd and his companions are kidnapped by a Mad Scientist who looks and acts exactly like KFC's Col. Sanders, and had an army of mutants identical to various 20th century corporate mascots. Both drew complaints from the trademark owners and the publisher, within weeks of their publication, offered to sign legal documents stating they would never let the stories be reprinted in exchange for a promise not to be sued over them. When a recent US oversized hardcover was published collecting Brian Bolland's Dredd stories, the collection had to outright state on the back cover, that "The Complete Brian Bolland Judge Dredd" title wasn't actually true, due to the there being two stories they were legally unable to reprint.
The comics business is always changing, with canceled series, editorial changes, and Executive Meddling all frequent. As a result, a number of comics stories are commissioned and completed (or nearly so), without ever seeing print. This includes "inventory stories," which are intended to be published only if the regular team is late. After a while, unused inventory stories tend to "go stale" due to subsequent changes in continuity. Some examples:
One of DC Comics' rarest titles fits, even though it was published... technically. DC canceled a large number of books in the "DC Implosion" of 1978, so suddenly that a large number of completed stories remained. Canceled Comics Cavalcade put many of these stories into publication for copyright purposes, but the series "ran" for only two issues, each with a print run of only 35 issues. A few of these stories eventually saw publication in "regular" DC titles, but most remain effectively "lost" to this day.
The Marvel/DC crossover title JLA-Avengers was first scheduled for publication in 1983. The story was plotted, and George Perez completed 21 penciled pages of art. Due to editorial disagreements between the two companies, the project was canceled. In subsequent years, as editorial regimes changed, there was occasional talk of reviving the project, but to no avail (likely due to, among other reasons, changes in the teams' rosters during the intervening years.) Eventually, the project was revived, but with a new story and completely new art by Perez, in 2005.
Some Golden Age comic books have been entirely lost to time, due to poor quality paper, limited print runs and nobody saving them for posterity. Many were lost in the paper drives of World War 2, with the first thing to go was the old comic books that been gathering dust. This is also why copies of Action Comics #1 have sold at auction for over a million dollars; only 50-100 copies are thought to exist today.
In 1989, as part of a time travel storyline, Swamp Thing was going to meet Jesus of Nazareth in issue #88 of his title. Writer Rick Veitch wrote the script, penciller Michael Zulli at least partially completed the artwork, and the story was approved by editorial, but then DC's publisher killed the story, deeming it too inflammatory. Veitch ended his relationship with DC over the controversy, and neither the Jesus story nor the resolution of Swamp Thing's time travel adventure was ever published. The script and existing artwork for the story, "Morning of the Magician", can be seen here.
Superman #712 was scheduled to contain a team-up between the Man of Steel and a young Muslim superhero named Sharif (actually a revival of an obscure young hero from the '90s who went by the name "Sinbad," now several years older), but the story was pulled after Action Comics # 900 (which featured Superman renouncing his U.S. citizenship) drew unexpected controversy from the media concern that DC was trying to make Superman "un-American". The Sharif story had some early editorially-mandated changes, such as the vetoing of the original idea that Sharif would wear Superman's "S" shield, but with the Arabic letter, before the entire story was nixed. Amusingly, DC tried to claim (through leaks to comics gossip blogger Rich Johnston) that it had nothing to do with religious issues. Instead, the supposed rationale was the fact that Superman rescues a kitten from a tree in the story. Supposedly this story element was "too corny and heavy-handed" for DC Editorial. Can you guess what the very first thing Superman does in Superman #713 was?
Orson Scott Card was supposed to write an issue of Adventures of Superman, but the story was shelved indefinitely after the Internet Backdraft DC received over hiring a noted person with anti-gay views. The issue's artist even walked away from the project after the furor started heating up.
The Wonder Woman graphic novel Hand of the Gods was supposed to come out in late 2011. Perhaps it would have been shelved anyway due to inconsistencies with DC's New 52 relaunch, but the arrest of artist Josue Rivera (who works under the pen name Justiniano) on child pornography charges probably makes that permanent.
The original run of Teen Titans had its twentieth issue rewritten and redrawn after Carmine Infantino objected to its story's heavy-handed messages about racism, fearing that they'd lose potential buyers in the South. The original writers Len Wein and Marv Wolfman wound up in trouble over the controversy and found themselves blacklisted from DC for about two years (though Wolfman was at least given the chance to write Donna's first origin story in a later issue). The original story included the debut of a black superhero named Jericho, who was changed to a white man named Joshua in the version that saw print. Wolfman would later reuse the Jericho name for a character he'd create in the '80s Titans. Although some pages of the original artwork have been posted online, the entire original issue may never be found.
A number of Grendel issues are apparently unlikely to be collected, as the original artwork has deteriorated too much.
Wild CATS/Aliens has become this again. It was omited from the first round of Stormwatch TP Bs, then was licensed for the second printings, but was omitted from the recent hardcover collection. Worse, the text summary from the first printing of the final Stormwatch trade was omitted from the hardcover.
It's a point of much frustration among the Doctor Who fandom that Endgame, the first of four volumes collecting the Eighth Doctor comic strips, is so far out of print that it might as well be a lost Patrick Troughton episode.
Suske en Wiske: The story "De Gekalibreerde Kwibus" is missing from the regular series and only available in the separate "Suske en Wiske klassiek" series.
It appears that Archie Comics is attempting to do this with Archie Comics' Sonic the Hedgehog issue #50, the final part of the EndGame storyline, as the recent reprints of the final part replace the cut up version with the superior one from Sonic Super Special issue #6. Other stories not being reprinted include "The Last Game Cartridge Hero" from Sonic Live, the entirety of Sonic Super Special issue #7 (which was a crossover with Image Comics), the story "Ghost Busted" from issue #8 (which was an adaptation of one of the Sonic Sat AM episodes, and both parts of "Some Enchantra Evening" from issue #10, the first part of which started over in Sabrina the Teenage Witch.