The feeling is pretty much universal among fanfic writers who keep it up for any period of time. It's not unheard of for the latest update of a Long Runner to casually mention that the author now finds the opening chapters to be complete crap, and many a Dead Fic only remains dead because the author can't stand looking at it anymore. But here are some specific examples...
Notorious furry Sage Freehaven. As a teenager — and prior to entering the Furry Fandom — he wrote several awful Chip 'n Dale Rescue Rangers fanfics called "The Dark Savior Saga", which saw various revisions over his tenure in the fandom and contained innumerable examples of bad fanfic tropes; he also made the mistake of writing them under his real name, only later changing them to bear his Furry Fandom pen name. Years later, he had the entire series — and anything else associated with both that name and his real name, including a MiSTing of the first fanfic in the series — stricken from the Rescue Rangers fandom's fan works repository. The only place you can read any of it now is at Everything What Is Crap, where the MiSTing of the first story in the series (found under the "American Works" section) remains intact.
GeminiStar01 has been hovering around Fanfiction.net for six years now, starting with the second season of Digimon and YuYu Hakusho fics. Don't bring them up when talking to her, unless it's in person and you want to see the funny color she turns.
Eyrie Productions Unlimited's first project was Undocumented Features, a work they are still continuing 20 years after it started. However, their second was the spinoff(Gryphon and Zoner get) Hopelessly Lost, something that the original authors would prefer to have you forget (and which they are, in fact, recreating as Bubblegum Crisis: The Iron Age, a markedly superior work). Also, within the Undocumented Features body of work, the authors aren't too fond of the initial stories, which had started as a silly blend of wish fulfillment and in-jokes; Gryphon has referred to them as his "crap period."
Author razzamatazz73 actually changed her penname because she was so embarrassed by her old fanfics. She even mentions on her profile that her general rule of thumb is to ignore just about everything published before 2007. Her newer material is noticeably better, considering her rather cliched first fics and more recent Star Trek and FusionFall successes. Her review responses to her older stories are particularly amusing, as she usually begins all responses by apologizing to the reader.
Andrew Dickman created a short flash animation called Rockman Neo. He intended to create a Darker and Edgier fanfic and fan game based on the Mega Man series. However, after some time, Dickman abandoned the project. Not only that, but he started becoming outright hostile to fans who asked whatever happened to Rockman Neo.
The first multi-chaptered installment of the For Good 'verse underwent a drastic rewrite as well as a change of titles, from Watermark to Breakaway. The author cites bad writing, among other things, and is embarrassed in general at the BLoSC fics she wrote when she first entered that particular fandom.
There was once a Sonic babyfic by Aerogreymon8.0, titled Eggman's New Invention, about Eggman inventing a weapon that turns male people into babies and the female characters having to take care of them. It got taken down somewhere between November 2005 and early in '06. When contacted (that is, while he even went by the aforementioned penname; unknown whether he changed his name or deactivated his account altogether since then) he stated that he was rather self-conscious about it.
My Inner Life appears to be this for Link's Queen. She now derides it as something stupid she did when she was younger, and hates talking about it.
Cori Falls apparently laughs at her old stories now.
John Nowak, creator of The Nowakverse, began his MST of Under The Bridge (the first story in the series - which he wrote!) by describing himself as someone who should never have written Rescue Rangers fanfic. He would go on to insult the story in other MST works, as well.
Stephen Ratliff, creator of Marissa Picard, was mostly enthusiastic about his creation... except for one story involving her. One MST of the story "Time Speeder" opens with a quote, taken from a Star Trek discussion group, where Ratliff states he never should have written "Time Speeder".
Part of why Cyber Commander wrote a remake of Yu Gi Oh The Thousand Year Door was to purge it of the character Wanda Underwood, whom he came to despise for being a needless Take That at Weevil. There were other parts of the old version he hated, like having Raven use a Dark Scorpion Deck with three new members on the team (violating the Five-Man Band status of the group). He has also forbidden any other authors from using those cards.
"Sonic The Hedgehog: The Series". The author has pulled it from all online sources and deleted personal backup copies. It no longer even exists and the author has stated regret for spending time on it.
Avenging Hobbits, the author of the Harmony's Warriors series, decided that the original version of Iron Mare was of such poor quality that he declared it Canon Discontinuity (even using the term), removed it from FimFiction, and rewrote the whole thing.
(On her old Frollo fics) "Warning! The early stuff – e.g., the "Claude & Me" series – is blatantly and awfully Mary Sue-ish. I hate it."
Despite gaining a fair amount of praise, Steve Worek, creator (and mostly unseen co-star) of The Rocky Horror Picture Show fan film "Bedroom Scenes" generally scorns any discussion of it. The theme song for the upcoming sequel, sung to the tune of 'Science Fiction Double Feature,' urges viewers to forget that "Bedroom Scenes" exists.
Frustratedstudent, the writer of the Les Misérables fanfiction "A Thenardier's Redemption" was mortified enough to do a rewrite of the entire thing, and pleads youthful innocence for some of the events there.
SiFi270 has disowned Snow Angels and deleted it from fanfiction.net, and will mock it in his later fan fics every chance he gets. As far as he is concerned, the Recursive Fanfiction written by Racke is infinitely better.
Pretty Cure Perfume Preppy is one of the most famous and polarizing fan fics in the entire Pretty Cure fandom. It was so famous that it started a trend of people making their own fanseries. At first, its creator, Cure Shabon, was proud of it. But after many years, she now realizes how cheesy and flawed it really is, and doesn't consider it her best work anymore.
Despite receiving near-unanimous praise during its active phase, the "Metroid" / "The Legend of Zelda" crossover fanfic "Life of Samus" has become its author's standard for terrible writing. Every instance of it being mentioned now is in an overwhelmingly negative context.