Before Garfield, Jim Davis did a short lived comic called Gnorm Gnat. Davis thought it was funny. Not a lot of other people did. After one editor told Davis that "no one can relate to bugs", he pretty much gave up, and the final comic had Gnorm stepped on. The only times Davis brings the comic up now is when he's mocking it as "one of his biggest mistakes". This was lampshaded in one of the Garfield book collections. A gag comic at the end of one book was titled "Top 10 Comic Strips Jim Davis tried before Garfield" where Number 2 on the list was... Gnorm Gnat. The number one comic strip "tried" was Garfield being a living toaster.
Bill Watterson claims he regrets introducing Calvin's Uncle Max into Calvin and Hobbes. His reasons are that Max didn't have much of an identity, he didn't bring out anything new in Calvin, and the awkwardness of Max not being able to address Calvin's parents by their first names (which Watterson, as a matter of principle, didn't want them to have).
Berke Breathed, creator of Bloom County, kept a great deal of the strip's first two years out of publication for years because he thought the strips were dated, unfunny, poorly drawn, derivative of Doonesbury, or some combination thereof. Finally, in the late 2000s, he began releasing complete anthologies of the strip, complete with running commentary. Even in the commentary, he is highly critical of his own work, saying that he had no idea which direction the strip would take until around 1981, when Opus the penguin became a permanent cast member.
Berke's first strip, printed in his college paper, was such a great source of shame to him that he allowed only about thirty strips from it to be printed in the Bloom County libraries—the vast majority of which were to show the origin point of gags reused in Bloom. The Acadamia Waltz was collected in two volumes, and according to Breathed's bibliography on his site: "eBay is your only hope." When IDW (who published the other collections of Breathed's work) finally got the rights to republish The Acadamia Waltz, the cover consisted of Opus opening a box labeled "Don't EVER@#?!* open this -BB", and the collection itself is titled Academia Waltz and Other Profound Transgressions.
In a crossover with this, literature and animation, Berke does not like A Wish for Wings That Work, an Animated Adaptation of his 1991 Christmas book of the same name (which in turn uses the Opus character from Bloom County and Outland).
Early on, Pearls Before Swine was a webcomic. Most of it was re-drawn/re-written and published to newspapers, but quite a few were also left out. Stephan Pastis republished some of those webcomic strips that were left out in a book, and spent most of the time pointing out how Out of Character everyone was and how bad the art was (even for his minimalist stick-figure style).
Scott Adams released a series of Dilbert strips that are really contrived to give Dogbert an arch-nemesis named Bingo the Cow Herding Dog in order to give Hollywood some material to work with. It would have turned the strip into something only other cartoonists like. This was during strip's early years that focus more on Dilbert's antics at home than at work. You can read them here.
In a twentieth anniversary collection, Scott Adams included some comics he wrote for Dilbert as practice before trying to find a syndicate. Before listing the examples, Adams wrote "At the time, I thought puns were the highest form of humor. Forgive me."
Charles M. Schulz frequently said he was somewhat embarrassed by the first few years of Peanuts. As a result, several hundred strips from the early 1950s were never reprinted in book form during his lifetime, only seeing the light of day via Fantagraphics' Complete Peanuts series.