Comic books and comic book storylines that are all but universally considered terrible often end up being mocked in another comic book from the same company or even the same comic book series from which the reviled story came.
Jordan: Superman was overrated. Too wrapped up in himself. Thought the world couldn't get along without him.
Stan Lee has remarked that Spider-Man regular J. Jonah Jameson was based on how Lee imagined the fans viewed him: a cantankerous, money-hungry old man. Most comics fans today see Lee as an affable grandfather figure, so in this case the Self-Deprecation lost its relevance. Likewise, Jameson received multiple bits of character development over the years, painting him as harsh, aggressive, and sales-happy, but also honest, fair, and with a strong moral code. As a result, he ceased to be an effective parody.
In Marc Guggenheim's Civil War: Choosing Sides, Mac Gargan is discussing selling his life story. He wants Guggenheim to do the movie, then says "No, the other Guggenheim, the one who wrote that hockey movie", simultaneously putting down Marc himself, and giving a Shout-Out to his brother Eric.
Kurt Busiek and Erik Larsen's early 21st-century resurrection of The Defenders: In addition to portraying its principal characters as supreme Jerk Asses who eventually decide to take over the world so it won't need to be defended (and, more importantly, so they won't have to deal with one another), the series invoked Stylistic Suck via references to Marvel's incredibly goofy Silver Age giant monster comics, and one of its covers proudly boasted a Wizard Magazine quote proclaiming The Defenders to be "the worst comic ever produced."
During a New Avengers arc dealing with The Multiverse, Johnathan Hickman wrote a scene where Beast claims that Multiversal and For Want of a Nail concepts tend to be the foundation of "Every piece of bad science fiction ever written".
French cartoonist Gotlib never misses an opportunity to make fun of his own limits as an artist. For example, while discussing the Italian westerns, he drew a typical protagonist of such films, which suspiciously looked like a famous actor... and commented it with "Any resemblance to Clint Eastwood would be one hell of a fluke" — a jab at Gotlib's (self-perceived) poor skills in caricaturing real people.
Johnny the Homicidal Maniac is a huge source of Old Shame, one Squee comic sends the titular character on a rant about how sometimes it seems like his life is controlled by a "suckish cartoon guy who can't draw", and one Invader ZimDVD commentary track has one member of the voice cast remark that "Jhonen is genius, although I couldn't say that in front of him because he'd beat me up or something." Back when he was planning on making a movie (whatever happened to that?) he said it'd be "Coming soon to a bargain bin near you."
For bonus points, he regularly uses the margins of his own comic to snark at elements of his writing and art he dislikes. During a particularly melodramatic bit of Wangst from Johnny, for instance, a caption remarks that he's "regressed back to stupid teen angst mode"; his caption to some odd flying creatures in the background of heaven admits he has no idea what they are or what he was thinking.
During J. Michael Straczynski's run on Spider-Man, one comic included a security guard claiming he dislikes Babylon 5 because of its Kudzu Plot. In another issue, he mocks his own Retcon of Spider-Man's origin by having the director of the "Lobster-Man" movie claim that said hero's origin via radioactive lobster bite is lame and orders the writers to change it to the hero being The Chosen One of a "Lobster God".
MAD called its writing staff "The Usual Gang of Idiots", published letters that insulted the magazine creatively, and often included shots on itself in articles. They were also well-known for putting pictures in their letters column of actors tearing up copies of issues that parody something they were in.
Craig Kyle and Christopher Yost put a grave of "Kyle Yost" in one of their comics.
In Ex Machina, Hundred interviews Brian K. Vaughan and Tony Harris for the possibility of them making a graphic novel style biography of him...then decides to get Garth Ennis and Jim Lee instead.
Ennis did something similar in The Boys, in which he tries to get a job at Victory Comics and is literally told to go fuck himself.
Joe Quesada: Tim, Axel, do you guys still read the comics we publish?
Axel Alonso: We still publish comics, Joe?
Tom Brevoort: First, it's Tom, and second, I like that one with differentcolorrings. Do we do that?
Garth Ennis here refers 2000 AD having its best ten years "before they got desperate and started employing people like me."
Evan Dorkin. Although he never holds back on letting people have it the biggest butt of all his jokes is always himself.
One issue of the New Avengers featured Nighthawk telling the titular team that there is no reason for them to be called Avengers:
Nighthawk: I don't get it! Clearly you guys are The Defenders, but you're calling yourselves The Avengers??? I mean, is it me? Am I the crazy one?
The same gag was used in an earlier issue where Hawkeye met the New Avengers for the first time. Upon seeing their roster, he confusedly asked if they were supposed to be the newest incarnation of the Defenders.
Ben Templesmith appears in the Wormwood Gentleman Corpse issue "Segue to Destruction" at the Dead Alley, where Wormwood describes him as "my biographer". None of the cast have any respect for him at all, and mock his defensively citing his three Eisner nominations: "No idea what those are, but he seems obsessed with them."
In Christopher Priest's first issue of Deadpool, the title character arrives in Limbo, dragging a bag. He then has to throw the bag, labelled "Everything that made this book good", into the void. He's greeted by various characters whose books Priest was writing when they were cancelled. They tell him that his own cancellation is now inevitable. In Priest's final issue, 'Pool again arrives in Limbo dragging a bag ... a body bag. When the other characters realise he's killed the writer responsible for ruining their lives, they all cheer.
Mr. Sensitive: Somebody is making fun of X-Force. Anarchist: Hell, that's our job.
In the 1970s, Cary Bates once wrote himself into a Justice League story arc (in Justice League of America #173 and #174) as a villain. Not a thinly disguised version of himself named Barry Cates, not an alternate universe version of himself, just himself from our universe, where he's a comic book writer (in-story, being transported from our "real" universe to the JSA's Earth-Two made him go insane). Fellow writer Elliot S! Maggin also appeared as a character in the story; he was portrayed in a slightly more positive light (i.e., not an insane villain).
Marvel's What The?! parody comic poked fun at their own plotlines and characters (they also took shots at DC, but less often). One issue even made fun of the hairstyles, by having "The Mighty Sore, God of Blunder" stumble into the barber who does all of them.
Near the end of Justice League International crossover "Breakdowns", Blue Beetle comments on the increasingly convoluted series of events the team is facing, saying that it seems like something a pair of mediocre comic writers would come up with. This sort of humor was commonplace in the series. A Running Gag involved former members of the "real Justice League" like Hawkman and Aquaman complaining about how the JLI was ruining their team's reputation by acting like a bunch of incompetent goofballs and jokesters.
Viz delights in describing itself as "not as funny as it used to be". From time to time it will also proudly say that it was rubbish then, too.
In the Hellboy story In the Chapel of Moloch, Hellboy is investigating the strange behavior of a painter who is making paintings of ghouls and demons. Unimpressed, his his only comment is "He is ripping of Goya". (And the paintings are exactly the same style as all the other monsters in the series.)
DC Universe: Rebirth #1 sets the stage to be a major one towards Watchmen by having the malevolent force that caused The New 52 be none other than Dr. Manhattan, causing the heavy cynicism of the 90s through today to be laid solely at this universe's feet.
Also, specifically, the Pre-Flashpoint Wally West says someone stole time, relationships and hope from the universe. This is exactly what people criticised the New 52 for: de-aging characters whose ages never factored into their appeal, the legacies of the DC universe (which Wally is actually the poster boy for), the removal of love interests and marriages, and the overall grim tone of the universe.
"Superheavy", the Batman storyline where Jim Gordon becomes Batman, had a very mixed reception from readers, mostly due to the chocie of Batman successor. When Bruce Wayne returns as Batman, he rescues Jim and says "who died and made you Batman?" Doubles as a joke between the two, of course, but the issue opens with meta commentary about Bruce Wayne's return. About how "the people" need "their" Batman back, and how it's up to "you" to deliver, with Bruce seemingly looking write at Snyder on the same panel.