The Boondocks. It would probably be easier to list the strips that weren't Take Thats against something or someone than the ones that were.
Bill Watterson has used Calvin and Hobbes to mock modern art, art criticism, and superhero comic books. Either Calvin uses phrases copied verbatim from art journals to describe his snow men, or his breathless praises of comic books as an art form are interrupted by comments like, "Oh no, Captain Steroid's getting his kidneys punched out with an I-beam!" Take note that Watterson's career peaked during the Dark Age of western comics, which likely influenced his opinions quite a bit, but as to why he didn't seek out fellow "comics can be art" proponents such as Dave Sim and Scott McCloud and join up with the Graphic Novel movement is a complete mystery.
Watterson directed a few Take Thats at Garfield creator Jim Davis over the years. In a rare 1987 interview, he harshly condemned Davis' comic strip U.S. Acres, calling it stupid and badly done. In The Calvin and Hobbes Tenth Anniversary Book, Watterson extensively discusses why he hates merchandising, and how it robs a comic strip of its heart and soul. He even writes about how a cartoonist risks becoming a "factory foreman", remarking on how he went into cartooning "to draw cartoons, not to run a corporate empire." He disgustedly remarks on how he would have sold out his own creation if he'd done this. Given the context, it was pretty clear who he was talking about. Granted, since Jim Davis stated that he created Garfield for the purpose of making money, and probably didn't intend there to be much of that deeper significance in which Watterson puts so much stock, it's unlikely that Watterson would have liked it anyway.
Bill Watterson's foreword to Bill Amend's first FoxTrot book is basically an extended take that against Jim Davis. For example, Watterson champions Quincy the Iguana for not thinking "the cute thoughts that quickly get most comic strip animals in the greeting card business."
Of course, one could also make the case that there are no Quincy the Iguana cards because the average person thinks Reptiles Are Abhorrent.
Watterson had Calvin reading from Chewing, a magazine that rated chewing gums in excruciating detail (e.g., "[T]he top five brands of chewing gum based on flavor retention, elasticity, bubble capacity, and chewing rebound"), offered advice for chewing it, and otherwise was a spot-on parody of every review mag.
Watterson made several strips with subtle jabs at his editors and the syndication people.
There is a Take That related to Calvin and Hobbes, although not in the strip itself. For strips in Bloom County that parodied cartoon cats that featured characters such as Garfield and Hobbes, Bill Watterson retaliated hilariously with this comic◊. In response Berke Breathed said this:
"I have committed other thefts with a clean and unfettered conscience. Garfield was too calculated and too successful not to freely raid for illicit character cameos. Calvin and Hobbes was too good not to. Calvin creator Bill Watterson took these thefts in stride and retaliated in private with devastatingly effective illustrated salvos, hitting me in my most vulnerable places. Bill's sketch is an editorial comment on my addiction to the expensive sport of power boating and the moral compromises needed to fund it. That's me doing the kicking. The chap on the dock represents my cartoon syndicate boss, which says it all, methinks."
In one comic Calvin talks about wanting to be a talk radio host. It ends with him saying "Imagine getting paid to act like a six-year-old!" The strip was published in 1994, right about when Rush Limbaugh was attracting a wide audience.
A mutual Take That! between Dilbert and Zippy the Pinhead: Bill Griffith used his daily strip Zippy the Pinhead as a forum to criticize Scott Adams' artwork as simplistic. Adams responded on May 18, 1998, by having Dogbert create a comic strip called "Pippy the Ziphead," "cramming as much artwork in as possible so no one will notice there's only one joke [and] it's on the reader." Dilbert notes that the strip is "nothing but a clown with a small head who says random things" and Dogbert responds that he is "maintaining his artistic integrity by creating a comic that no one will enjoy."
In another Dilbert example, Dogbert responded to a letter from a man named Dork who complained about his use of "dorkage" as an insult: "I apologize to all the dorks who were offended. I hope we can put this behind us."
The comic took a subtle shot at some of his critics and readers with a Sunday strip that saw Les Moore reading the Sunday comics to his bedridden wife Lisa, remarking "They always made you laugh. I guess that's why they're called the funnies." This was Tom Batiuk's response to critics' complaints about the recent lack of humor in Winkerbean, especially because of the "Lisa's cancer" storyline. He wasn't too pleased that people didn't like him slowly torturing one of his characters to death in what used to be a gag strip.
Several years earlier, he ran a plot critical of intelligent design that he used to take shots at a fellow comic author. When one of the teachers is forced to teach intelligent design alongside evolution against his will, two of the main characters discuss making a comic about it. One of the boys remarks that people might accuse of them of being "the anti-Johnny Hart," and then proceed to draw a very crude parody of B.C. with a pro-evolution slant.
Funky Winkerbean loves this trope. The most recent comics of this writing (9/14/2009) on for a couple of days, are basically one big Take That! at all the people who complained about the whole "dying of cancer" arc. The local school is putting on a production of Wit, a play about a woman who, surprise surprise, dies of cancer, which gets the parents up in arms and complaining how they came to the theater to be entertained, not depressed. The author basically writes them all into a strawgroup of his critics and then has his avatars talk "reason" to them (The reason being that plays about cancer are "true art" and Spam-a-lot isn't).
My Cage took a shameless swipe at this storyline showing Jeff's kid dressed as the Funky Winkerbean grim reaper for his own school player about cancer and death, as Jeff wonders what kind of "thoughtful" comic-strip could have inspired it. One week later, twomore strips on the subject revealed that the play was based on a comic called "Groovy Blinkerlegume", and Jeff and Max try to ponder why anyone would take funny strip and try to make it serious. At which point new character Sam the Sacrificial Lamb is killed on camera for a punchline.
Relating to the first one, there was another Crankshaft strip where Ed Crankshaft just flat out said "the comics are supposed to be funny," chastising his audience for not being amused by the eternal suffering of his characters.
Pearls Before Swine is pretty well known for take-thats, usually in the mouth of the resident Jerkass Rat, or the psychopathic Guard Duck. Popular targets are Cathy and Family Circus. The strip also mocks itself, so Pastis probably doesn't mean it... most of the time.
The Family Circus ribbing ultimately led up to a storyline in which Rat gets lynched by Family Circus fans, which is possibly another Take That! to people who don't appreciate 'take thats'. Or, even more meta, it could be seen as a Take That! against himself, in that Rat, a mean-spirited Jerkass, probably got what he deserved from those fans, quality of the Family Circus notwithstanding.
On such Pearls Before Swine storyline showed the Family Circus family harboring Osama bin Laden. Yes, it's Refuge in Audacity, but it manages to be funny while pointing out how glurgy and trapped in the past Family Circus is.
And, at least if Pastis' directors commentary is to be believed, Bil Keane actually liked those strips.
At a comics convention, Pastis was giving a talk, and mentioned strips using each others' characters, adding that it was all done in an atmosphere of mutual respect. Jeff Keane (now doing the strip) stood up and yelled "Go to Hell, Pastis!" and stormed out. It was all staged, of course.
Family Circus itself responded to Pearls Before Swine's Take Thats with a strip where the kids read a book called Pig and Rat Get Lost, which causes them to leave the room to watch TV.
On the announcement of the retirement of the comic strip Cathy, Stephan posted some ruminations on how the many Take Thats he had made early in his career, and how Cathy Guisewite responded. Mildly heart-warming.
La Cucaracha once did a subtle take that to Pearls. In a response to the strip where Rat wrote a letter to a comic syndicate saying strips appealing to minority groups aren't funny, La Cucaracha (one of the said demographic strips) did a Sunday strip a couple months later that features the main characters getting a similar letter, signed by "Steve Pasty", who is depicted as a redneck white trash. Unlike other examples listed, which are meant to be light-hearted, this one is actually meant to be critical of Pastis, and was drawn as a rebuttal to his points.
Liberty Meadows has often parodied other newspaper comics. While some of these parodies are affectionate, others are clearly take-thats. For example, one arc had Frank on a date with "Debbie the Psycho," a thinly-veiled Cathy stand-in who constantly babbled about swimsuits and her weight, nearly driving him suicidal. Other strips mocked the sentimental banality of late-period Peanuts.
While Sally Forth is known for being rather safe material, the current author Francesco Marciuliano tends to take repeated jabs at his competition using his own webcomic Medium Large. He usually does this by portraying well-loved icons in disturbing scenarios, but he once did a more pointed strip referring to Momma as "starring some squiggles and what may be a nose."
Mark Tatulli's Lio is known as much for its morbid sense of humor as it is for its parodies of other comics. He got a lot of interweb hits when he took a few shots at For Better or for Worse, but it may seem strange that he frequently shows his main character tormenting the kids from Peanuts. Not so much when you discover that he received a torrent of hatemail when a newspaper used Lio as a replacement for Peanuts reruns.
Al Capp frequently used Li'l Abner to deliver Take Thats to pretty much anything that bothered him. Within his own medium, his "Fearless Fosdick" character, a strip within a strip parodying Dick Tracy, stands out. Fosdick is portrayed as an idiot with a penchant for violence that just can't die. Eventually the in-universe creator of the strip is revealed to be completely insane and the strip a result of his violent fantasies.
Capp famously depicted a parody Mary Worth, who took a vacation from her strip (to her author's relief) to meddle in Abner and Daisy Mae's affairs. That strip then reciprocated, depicting Capp as a drunken lout.
After PvP creator Scott Kurtz announced he was going to offer his comics to newspapers, Non Sequitur had a strip involving a fat nerd named "Scotty" trying to get into a club.
Berkely Breathed's Bloom County, and its offshoots Outland and Opus, pretty much live for this trope, taking shots at both politics (Bloom County had Oliver's attempt to protest apartheid by turning the South African ambassador to the U.S. black) and pop culture (one story arc in Outland involved Mickey Mouse's sleazy cousin Mortimer getting fed up with the changes Michael Eisner was making at Disney, and beating the crap out of him).
It was inevitable that someone would do this regarding the Wii. According to FoxTrot, "Soon kids across the world will be rushing home from school so they can Wii."
FoxTrot has actually done a Take That against the entirety of newspaper comics. In one story, the father of the family is forced to confront the fact that the comic strip he loved as a kid, "Captain Goofball," has lost all its appeal over the years, and is simply no longer funny. It's basically the author's way of commenting on the way that there are so many comics in the newspapers these days which were once funny, once had a lot of appeal, but are now simply tired and boring ("Garfield" or "Family Circus", anyone?).
This is a much lighter Take That than many of the other examples on the page, in that Amend is willing to admit that they were funny. You'd never hear Watterson say that.
And he usually refrains from taking shots at specific comics in general, although he will give them some good-natured ribbing on occasion (like a strip poking fun at the political commentary in The Boondocks).
The March 23, 2014 strip makes fun of Candy Crush Saga, Farmville, and the mobile Dungeon Keeper in one fell swoop. Peter plays a game on his phone called "Candy Farm Dungeon" (with each word in the title trademarked as a reference to King.com's trademarking of the words "Candy" and "Saga" as applied to video games), and gets frustrated when the game keeps pestering him to spend money on tokens to complete simple tasks, reaching ridiculous heights when Peter finds out that he can't turn his phone off to stop the game from playing:
"Buttons sometimes break. Use 40 tokens to diagnose the problem."
Make of this what you will, but toward the end of Peanuts, Charles Schulz produced an arc in which Charlie Brown goes to renew Snoopy's dog license, and a few strips with other licenses sent to him. In the last strip, Charlie Brown was told that Snoopy didn't need a license for 'that', shown in the last panel: an assault rifle.
If anything, that was a "Take That" against the National Rifle Association.
Another Take That! showed up in one of a series of strips from the 1950s in which Snoopy was going about doing impressions (or "imitations," as Charlie Brown referred to them) of kids, animals, and celebrities. One of these acts had him (inexplicably) blacking out his eyes and curling his ears into round disks to impersonate Mickey Mouse. (When Charlie Brown quietly informs Schroeder of this, all we see him say is "Msssp Msss.") Initially it appears to be merely a Shout-Out, but Charlie's comment of "Frightening, isn't it?" turned it into a Take That!.
A 1973 sequence has Charlie Brown horrified to learn that the neighborhood adults had created "snow leagues" for kids, where teams competed with each other to build snowmen, including playoffs and the chance to play teams from other countries. Y'know like how sandlot baseball and other activities kids used to do for fun ended up becoming the basis for organized, hyper-competitive Little Leagues.
A 1973 "Mr. Sack" storyline (where Charlie Brown keeps seeing baseballs everytime he seems something round, including the sun) ended with him watching the sunset, where instead of a baseball, he sees Alfred E. Neuman instead! This was Schulz's take that to MAD Magazine, which always parodied "Peanuts" in their publication. It was a friendly ribbing in this case, since both parties respected each-other.
The April 19, 2014 edition of Get Fuzzy has Stephen Pastis calling Darby Conley to complain about similarities between their strips. Conley asks him to call back, then blocks his number from his phone. That was the result of an arc in which Conley stole Pastis's strips. It was a rerun, but it isn't sure from when. He does have the book it was in, though.
Alex Hallatt's Arctic Circle, being a comic that lives on Green Aesop, has several jabs at climate change deniers.
This strip has one against both climate change deniers and creationists.