Old Shame/Comic Books

Tintin creator Herge has a couple. The first, Tintin in the Land of the Soviets, is ripped off wholesale from a single book condemning the Communist regime and has extremely primitive art. The second, Tintin in the Congo, is considerably racist, even for its time, in its caricatured drawing of African characters and depiction of them as lazy and childlike, causing a furor in the UK when it was reprinted (there is also an ongoing legal case in Belgium trying to get the book banned as incitement to racism). Tintin's psychotic maiming of wildlife (blowing up a rhinoceros with a drilled hole and a stick of dynamite) is pretty hard to take as well. Herge recognized this in retrospect and begged for them to be left out of print. Unlike the Soviet adventure, Tintin in The Congo was later redrawn and republished in color and with Herge's later more polished art style. The rhinoceros was spared in the Scandinavian edition and the English color edition. A third example is Shooting Star, created during the Nazi occupation of Belgium; it originally featured stereotyped Jewish American villains who were subsequently turned into generic villains.
The 1930s Mickey Mouse comics count as this, since many of them contain racist stereotypes, Mickey attempting suicide, and other themes contrary to the image of Mickey Mouse today. Because the comics themselves were believed to be in the public domain, Eternity Comics, an independent company not affiliated with Disney, attempted to anthologize "The Uncensored Mouse" in comic-book format in 1989 without permission from Disney, doing everything they could to prevent a lawsuit (using all-black covers, shrink-wrapping them so nobody would flip through the books, acknowledging Disney's rights in the copyright page, etc.). They were shut down anyway, because even if the comics were in the public domain (which is questionable), the characters weren't.
Jhonen Vasquez, author of Johnny the Homicidal Maniac, Squee, and co-creator of Invader Zim put out a single-issue "throwaway" comic called the Bad Art Collection, which was exactly what it says on the cover. When someone brought a copy to a signing event at a convention he responded with his usual good grace and humour; and commented, laughingly, "Oh my God, someone actually bought this thing," while signing it. According to Vasquez, the origin of the collection was him writing the cartoons back in school in order to get people to stop bugging him to draw for them.
Mexican cartoonist Rius published many comic books in the 60-70s. Being a firm believer in Marxism, he dedicated much of his work to socialism/communism and prophesized the fall of capitalism. One of the most famous examples of this is the book he made under orders of the Cuban government about the Cuban Revolution. After the fall of the Berlin Wall and the collapse of the Soviet Union, he admitted that he had to eat his own words and that he never drew anything negative about the socialist states of the time because, in his own words, he "didn't want to provide ammunition for the Imperialism."
For a long time, this was the attitude Mark Millar took towards a collection of early strips he wrote for Sonic the Comic in the nineties, insisting that he only wrote them for the money to pay for his wedding. He seems to have softened his stance on them lately, though.
Even though he hasn't taken it out of publishing, David Herbert would like everyone to forget Warriors of the Night, which is his first graphic novel.
Kurt Busiek accompanies his signature on copies of Spider-Man/X-Factor: Shadowgames with the refrain, "I'm sorry, I'm sorry, I'm sorry..."
Andy Schmidt formally admitted that The Transformers Continuum was of poor quality, but thanks to Denton J. Tipton and Carlos Magno making fun of him over it at the IDW offices, he wasn't allowed to forget it.