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. The story has since seen the light of day as a black and white version, in various Hellblazer TP Bs in the 2010.
Many comics that feature licensed non-Marvel/DC Universe characters (for example, Marvel's 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 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 (Marvel couldn't reissue Tiny Toons comics due to Marvel's rivalry with DC) unless the character owners reach a deal with the publishers. Star Wars was formally not reissued by Marvel until they got the rights back from Disney when Disney bought Lucasfilm.
It appears that Archie is attempting to do this with issue #50, the final part of the "End Game" storyline, as recent reprints replace the original 22-page cut with the superior version from Sonic Super Special issue #6. Other stories not being reprinted include "The Last Game Cartridge Hero" from Sonic Live† (for a plethora of reasons – including being universally hated, the usage of caricatures of real children, and the idea that the characters are just from a video game), the entirety of Sonic Super Special issue #7 (a crossover with Image Comics)† (not only because of the usage of Image heroes, but also because it used characters from a failed comic series writer Ken Penders was pushing), the story "Ghost Busted" from issue #8 (which was an adaptation of one of the Sonic SatAM episodes† (due to its questionable art style), and both parts of "Some Enchantra Evening" from issue #10, the first part of which started over in Sabrina.
Archie's Sonic series 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 had to settle. The actual damage remains to be seen, but Archie went ahead 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 comics business is always changing, with cancelled 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 cancelled a large number of books in the "DC Implosion" of 1978, so suddenly that a large number of completed stories remained. Cancelled 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 being 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. Allegedly it was due to the fact that DC was terrified of being targeted by the religious right, who at the time were engaged in a major PR war against Martin Scorcese over "The Last Temptation of Christ" and DC felt that Veitch's story (which implied Jesus's powers were described by Swamp Thing as magic based and where the Three Wise men were actually demonically possessed assassins from Hell) would garner a similar PR shitstorm. Veitch quit the book on the spot, forcing the series to go on a brief hiatus while DC scrambled to find a replacement writer (Doug Wheeler), who quickly churned out a replacement script that saw Swamp Thing returned to his proper time. While DC has attempted in recent years to court Veitch back to the company, and even started to work towards reprinting Veitch's Swamp Thing run, it all fell apart when DC told Veitch that they would not reprint the original version of #88 in his final trade (resulting in the planned trade for #80-87 to be cancelled, leaving the issues to this day not collected). 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 writer with noted anti-gay views. The issue's artist even walked away from the project after the initial controversy began.
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.
WildC.A.T.s/Aliens has become this again. It was omitted from the first round of Stormwatch TPBs, 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.
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.
With Joe Books' George Lucas Altered Version of Boom's Darkwing Duck comics, Dangerous Currency stands out as the only one not being reprinted or rewritten. It's even been declared Canon Discontinuity. Some sources say that the story wasn't approved by Disney. If you didn't get it when it was first released, hope you like spending lots of money.
A crossover between Wonder Woman and Xena was written and illustrated in the 90's, but for one reason or another, it's never been released.
Scott Lobdell and Aaron Lopresti completed an X-Men mini-series about the original Thunderbird back in 2000, but thanks to a host of unforeseen circumstances, it was shelved indefinitely.
While Suicide Squad is finally getting reprinted due to the upcoming movie, several side stories from the original series remain lost. These include Firestorm #60-64 and Annual #5 (of which, #63-64 and Annual #5 feature the very first fight between the Justice League and Suicide Squad and explain what exactly happened to Parasite after he's seen in Suicide Squad #1), Spectre #10/Captain Atom #11/Firestorm #68 (which tie into Suicide Squad #9, as far as the three issues, plus Detective Comics #582 and Suicide Squad #9 all take place at the exact same time frame and explain critical plot points that are critical to the Suicide Squad story but are never explain in the book) and Nightshade's origin story from Secret Origins #28
The 90s Clone Saga has become this. Reprinted in twelve volumes costing around $35/40 a piece, the books (titled "The Complete Clone Saga" and "The Complete Ben Reilly Saga") quickly fell out of print and go for over a $100 a piece.
"The Trial of Yellowjacket" is another out of print trade and one of the most infamous Avengers stories ever reprinted. Adding to the annoyance for those who did not buy the book, before it went out of print, is that it would have been the subject of the 10th volume of the Essential Avengers line. But the Essential line has been cancelled and no one knows when or if the book will be reprinted.
Incredible Hulk #296-297 were only partially reprinted, due to the issues featuring ROM the Spaceknight. They would have been skipped entirely if not for the fact that they had major plot advancement that was required reading, hence them appearing in TPB form in severely redacted form.