The most famous instance of this in the world of anime is Hideaki Anno and Neon Genesis Evangelion. The first half of the show was made while he was deep in depression over his career and the otaku lifestyle of the time. The atmosphere is bleak and moody, but also calm. Everyone has problems but they are downplayed as the series goes on and takes a turn for the optimistic towards the middle. The second half was when he was going through therapy and started to recover. Shinji becomes suddenly competent and gets eaten twice and is completely shattered after Kaworu's appearance and death. Asuka gets mindraped and her massive, massive issues are revealed. Rei's emotional development is undone because she dies to protect Shinji, and the Rei from the end of the series is a clone with her own issues. Misato finally rekindles her romance with Kaji only to have him shot the next episode and spends the rest of the series crying, completely broken - it's like all the bottled emotion in the first half gets let loose, as everything the series has shown so far gets deconstructed in the second half. Anno's efforts to understand his own troubles also shows in how the last two episodes put the cast through a psychological examination. Finally in End Of Evangelion, Anno included quite a few Take Thats against the sections of his audience that he had come to hate.
All this makes Rebuild of Evangelion a shining example of Creator Recovery. Hideaki Anno is now well adjusted, Happily Married to the manga artist Moyoco Anno (Sugar Sugar Rune and the last part of Helter Skelter), and the director of a very successful franchise. The atmosphere is less bleak and carries more energy, the characters are more stable and the story is not unrelentingly downbeat. Yet they are still just as dark, in some ways darker, as characters change and make choices, but not always for the better.
The other (in)famous example is Yoshiyuki Tomino. Reportedly, the famed director struggled with depression for decades, and this was expressed by the high body count of many of the series he directed, such as Space Runaway Ideon,Aura Battler Dunbine,Zeta Gundam, and Victory Gundam. Not surprisingly, this earned Tomino the nickname "Kill 'Em All". In his defense, however, he likes to do what he can to ensure that his series will not have a sequel. After his battle with depression, his work lightened considerably, producing stories like Overman King Gainer and ∀ Gundam, which contain positive messages and very few deaths. Gundam: Reconguista in G is a relatively by-the-numbers Gundam story, but is said to be expressly aimed at new fans and features a peppy ending theme that shows the entire cast, hero and villain alike, participating in a kick-line.
One of the big rumors surrounding Mobile Suit Victory Gundam claims that Tomino was intentionally trying to sink the Gundam franchise, in particular by making it dark and depressing as well as trying to deny Sunrise their merch money by having the villains' mobile suits be so ugly as to be completely unmarketable. Tomino would himself at least partially confirmed the rumors, having spoken several times about regretting making Victory too dark and cynical, and that it should definitely be seen as a product of his mindset at the time.
Like Anno, he remade Zeta Gundam into a movie series but with a happier ending after he got over his depression.
Kubo's first manga Zombiepowder. only lasted four volumes due to low sales. In a veiled reference on the inside cover of the final volume, Kubo acknowledged a nervous breakdown also contributed to its cancellation.
The author of Bitter Virgin, Kusunoki Kei, explains that a story arc of a character's stillborn child was drawn from experiences after her own miscarriage. As it is often with Creator Breakdowns, the writing has emotional honesty and power, which stands out in the story's extremely melodramatic tone.
Osamu Tezuka's, in the wake of personal betrayal, having his manga altered in serialization and anime adaptations, and health problems. His stories always had a certain 'edge', but you can see him subverting and deconstructing the ever living life out of some of his previously innocent characters and archetypes. The most blatant product of this is Alabaster.
On a more humorous note, it's been joked (and outright stated) by the anime staff that the reason the amount of fanservice spiked upward was because of Oda getting married to a gorgeous Ex-Cosplay Otaku Girl like Chiaki and being horny for her all the time - and to the displeasure of fans who liked the general lack of such things in the manga early on. For a guy who prefers not emphasizing romance that's not an obvious huge joke in his stories, he sure is a massive softie for his family.
More of a fanwork example, but the doujinshiTakotsuboya K-On! Trilogy involves Azusa being unable to find success as a musician, Mio being extremely jealous at Yui for her success, and Ritsu resigning herself to a low-level job because she believes she lacks talent. All of these can apply to the creator, TK, who tried for decades to become a published mangaka, but never could.
In 2006, nitro+' Gen Urobuchi confessed in his afterword to the first volume of Fate/zero to a loss in the ability to write heartwarming stories and a "tragedy syndrome" which compels him to make things tragic for the characters he conceived. He has later explained that childhood trauma from a near-death experience is at least partly responsible for this. Such tendencies showed up in spades in Fate/zero, which was a much darker prequel of Fate/stay night, and then, in 2011, in Puella Magi Madoka Magica. Judging by the Bittersweet Ending of that anime though, he appears to have gotten better, though it's up to the individual's thought of whether or not he's fully recovered judging from his later works. This bit of information would explain a lot about one of his earlier works, Saya no Uta in which the protagonist also survived a near death experience.
In 1972, Go Nagai released 2 manga around the same time: Devilman and Mazinger Z. The former was something that he considered to be his greatest work, while the latter's popularity heavily overshadowed it at the time. Toward the end of Devilman, his depression got the better of him and left the series with an ending that would put Anno to shame. Amusingly, the series became much more popular after its run finished.
A Fan Sub example: the final two episodes of LIME Anime's subtitles of Strawberry 100% begin with detrimental messages from the subber: "We recommend you stop watching now! Please watch something else!" on Episode 11, and "Why did you download this? It sucks!" on Episode 12.
Cat Soup was based on the works of the female underground manga artist Chiyomi "Nekojiru" Hashiguchi. She and her husband Hajime Yamano made a lot of really dark, twisted and weird stories in which the hate for society and culture in general were very common. And then, in 1998, Nekojiru commited suicide under really mysterious causes, and that very same year, an anime based on her works, called Nekojiru Gekijou, was broadcasted on Japanese television in the form of 26 short animated sketches, portraying that very crude humor and disgust for society in general.
She did have a breakdown during Time Stranger Kyoko. She was suffering emotional problems and didn't feel like she could give it her all for the manga, with her even asking her publishers if the series could be ended a bit early. This led to the entire series being only three volumes long, for the last six Strangers to just be brought in and appearing, and for the revelations of the story to be rather hurried.
They went through one when they were working on Fushigi Yuugi: Genbu Kaiden. Watase was thinking of maybesparing Takiko's life, but then one of their best friends died in an accident, and they decided to go "Status Quo Is God" and kill Takiko off.
Watase had another when working onArata: The Legend, since their editor during the Suzukuwa arc (named "Mr. I") was so exigent that he constantly ordered them to redraw pages and story the way he wanted and not how they planned because he didn't understand their ideas and thought Viewers Are Morons. Watase was so mentally and physically exhausted that they considered quitting manga business as a whole over the mistreatment, but thankfully, "Mr I" was replaced by new editor whose was more understanding and didn't interfere in their work during the Yataka Arc.
The novelist Kyouko Mizuki has said that she wrote the original Candy Candy novel, which would later become a manga series, as a consequence of the deep effect that her parents' deaths, especially her mother's, had on her:
"I lost my mother when I was 21, then I was all alone in the world. To write the story healed my sorrow";"Before I wrote the story of Candy, one of what some decided was "Who is her mother is not the theme". Whoever are your parents, you must accept your destiny and stand on your own feet—-I wanted to say so. When I started to write the story, it was two years after my mother passed away. My father passed away at my 12th year, I lived in solitude because I am the only child of them. Looking back on my years of writing Candy story, I realize that I healed my pain by writing".
During the production of JoJo's Bizarre Adventure: Vento Aureo, Hirohiko Araki was going through one as a result of mental problems at the time. This ultimately didn't have much of an adverse effect on Vento Aureo, but Araki had originally planned for Pannacotta Fugo to be revealed as The Mole, being a spy working for The Boss and trying to actively dismantle Team Bucciarati. Araki realized that the manga had already become somber enough as is and backed out of this depression-fueled idea, instead opting to have Fugo be Put on a Bus.
Bakuman。: Ryu Shizuka, author of "True Human" (a manga about the conflict between the "true humans" and the normal "old" humans), kills off all the human males and focuses the story around the young women serving the "true humans" around the time he starts going to cabaret clubs and socializing with the hostesses. His editor takes him to a tea date with Aoki and her assistants, along with Hiramaru and his editor, which turns out to be quite awkward due to Shizuka's poor social skills and gloomy demeanor. Shizuka realizes that the hostesses were only paying attention to him for money, and plans on writing about their false love in "True Human".
Yusuke Yoshino of CLANNAD. Meeting a group of kids in a hospital that are fans of his music made him question his singing for his own sake, preventing him from writing new songs. Then, when the biggest of said fans committed a huge crime, he blamed himself and let that bitterness crawl into his work. It eventually led to a downward spiral where he left the music scene a broken man.
In Princess Tutu, Drosselmeyer traps the entire town of Kinkan in a story after the villagers began to fear his story-turning-into-reality powers and cut off his hands. That story? Written with his own blood from the stumps of his arms where his hands were cut off. Which, of course, explains why the man is so insane and obsessed with tragedy.