Calvin and Hobbes featured a few of Bill Watterson's conflicts with his syndicate, publisher, and others in the form of Calvin arguing with his parents, frequently showing odd perspectives and art styles to emphasize his point. In addition, Watterson took it upon himself to draw extra artwork for the book collections, which ended up being such an insane amount of pressure that he was forced into sabbatical a few times.
For Better or for Worse manages to subvert this, though arguably not for the better. Author Lynn Johnston started going through a mess of personal problems late in the comic's run. Her reaction to this, oddly enough, was to start writing material considerably less inflammatory and dramatic than what had made her famous. Her marriage falling apart apparently greatly increased her desire to see two characters finally getting married without all the usual hang-ups weddings in troperville are generally known for.
Then we got the ReFOOB, which was mostly reprints of earlier strips, with art and dialogue changed to cast the alter ego of Lynn's ex-husband in a bad light, and making it look like (even moreso than the first-runs) Elly is living a bored, insufferable existence with an uncaring husband and bratty kids. This is especially distressing as it literally rewrites history with a joyless existence.
Funky Winkerbean appears to be in one since it's been in a long spiral of depression ever since the main character's wife died of cancer (critics just replace the dialog with "Cancercancercancercancer"), to the point where the title character (who apparently isn't the main character) also has cancer, the charity set up in the name of the seceded character gets stolen (it gets returned), and the high school drama class is performing the play Wit, which the PTA thinks is just too much (as do the critics). Oh, and a dead Iraq war vet isn't dead after all and returns just in time to learn that a loved one has died (probably of cancer) and that his wife has married another man.
The creator's other strip, Crankshaft, went through a week-long breakdown after his father died: Flash-forwards show Crankshaft as pretty much catatonic, confined to a wheelchair and living in a nursing home. At least his nurse was nice and took him out to see a ballgame (that was rained out). Flashbacks within the flash-forward show a much younger Crankshaft watching a ballgame (suggesting that he has retreated into memories of happier times, and is perhaps unaware of what is going on here and now). Since this is a strip where characters grow older, this has disturbing implications for Crankshaft. The next week featured Crankshaft being saved from a snake bite from his son-in-law's mother's yappy dog; it got better and so did the comic strip. It was eventually revealed that "future-Crankshaft" was actually someone else entirely, who eventually made another appearance. Misdirection or retcon? We may never know.
Another Batuik strip, John Darling featured a shock ending where the title character was gunned down by an unknown assailant in the next to last episode; the final strip is his stunned colleagues crying silently around his grave. This was brought on by disputes over the rights to the strip with the syndicate, with the character killed off to keep him from falling into their hands.
Spoofed in Jeff Kinney's novel Diary of a Wimpy Kid, in which the quest for a new cartoonist for the middle school newspaper was due to this. Wacky Dawg, according to the narrator, was originally a funny strip but the creator started using it to "handle his personal business" and was subsequently fired. The sample strip the reader sees has the eponymous dog, instead of saying something funny, asking the creator's girlfriend to forgive him for kissing one of her friends and reminding a guy who owes the creator money to pay up.
John Callahan was a newspaper cartoonist who got in a drunken car wreck at the age of 21, the result of a lengthy struggle with abuse and alcoholism and left him paraplegic. He gets it all out in a series of cartoons titled Will The Real John Callahan Please Stand Up?.