—Tara Lei Welker, Creator of Heart Core, talking about her first webcomic: Unsound of Mind.
Megatokyo author/illustrator Fred Gallagher is known for his self-deprecating remarks about his earlier work. His detractors once tried to use this to stain his reputation by revealing fanservicey early drawings of possible precursors to the comic's female characters; in response, he publicly revealed the whole "hidden" site, showing that he wasn't hiding anything - he was just embarrassed about his old art.
As mentioned above, before Heart Core, TL Welker did a gag-a-page comic called Unsound of Mind, where some of the central characters for Heartcore would originate from. She has long since discontinued UoM, and has stated whenever asked about it that she doesn't ever want to return to UoM. The closest thing one can find to Uo M in her deviantART gallery these days are the sidecomics of Heart Core, wich are written in a similar comedic manner.
However, she has released some of the earliest pages to donators of the comic, wich she gives in return for donations along with wallpapers.
As of late 2013, Welker has decided to go back and redo the entirety of Heartcore's first story arc (the beginning through Ame and Lutz leaving Asgard), being displeased with the original comic's art and pacing. To this end, the whole first arc has been deleted off of her website (although the original pages still exist on her deviantArt account).
Although Order of the Stick has always had simple art, it has gotten significantly better and more detailed as the series has gone on. Enough so that Rich Burlew has admitted that he hates having to draw the characters in their old styles (necessary for continuity purposes) when making bonus strips for the book collections. One design choice he particularly hates is the jagged lines that used to separate panels, so much so that he straightened them for the books.
In a non-artistic example, most of this strip is an apology for some of the sexist tropes that cropped up early in the comic.
Before his explosive popularity as a games critic, and even before his modest popularity as the creator of the Chzo Mythos series, Yahtzee ran several shortish webcomics on his site, which he has now gone on to disown completely along with every game he made before The Trials of Odysseys Kent, as well as every work of fiction he wrote before the age of 20, as he doesn't want people thinking he actually cares about said work.
In a Let's Play of the series on the Something Awful forums, he indicated that he doesn't stand by the Mythos these days either, but considers it an important step in his learning about games.
In its formative years, Platypus Comix contained no archive. Some cartoons were literally only up for one week and then vanished forever. The practice was originally due to limited storage space (it began as a Geocities site) but was continued until 2006 as a means of quality control (anything the author didn't regret making was given a position in a selective archive section). Most of the pre-06 works are still offline, but lately they have turned up in book collections.
Josh Lesnick, of Girly, took down his first comic down for this reason. As a result, a lot of people don't know there was a comic before Cute Wendy.
The author of My Roommate Is an Elf took down the comic for this reason. The art was painfully terrible and the writing was rough draft quality at best.
Ethan Nicolle, the artist that draws Axe Cop, feels that way about Jesus Christ: In the Name of the Gun (a comic he drew and co-wrote) since he considers it a crude joke that went too far.
Ian Jones-Quarty, who has since gone on to work as an animator, cited his embarrassment at early pages (which were artistically crude and sometimes fanservice-y) of RPG World as half the reason he elected to abandon the series. The other half was Creator Backlash over fans dislike his side project in the comic.
JJW, one of the old guard of early-2000 sprite comics, has built a blog dedicated to tearing them a new asshole.
Linkara has no problem bashing the first volumes of Lightbringer,admitting that not only is the art terrible (which is why he now outsources the artwork), but that the stories are excessively preachy. He invoked the Trope Name when explaining this on one episode of Atop the Fourth Wall, saying he was "stupid and full of myself and didn't know any better" when writing it.
This is largely how Shin-Goji of Twisted Kaiju Theater regards the K-Girls these days, a sentiment shared by most (if not all) of their actual creators as well, to the point of him removing the link to their galleries from the main site. However, out of respect for their fans (and those creators still attached to the characters), he still hosts the galleries on his site, although the link to them now exists solely on their deviantART fan group "Daikaiju Academy."
This is particularly amusing considering that among the artists disavowing their K-Girl connections are a major long-time furryyiff artist, another who's a regular contributor to Slipshine (focusing on dragongirls, no less), and an artist who specializes in hentai of Ash Ketchum and his mother.
Gina Biggs of Red String fame started a new webcomic, Demon Aid, in August 2013. Nine months later, she canned it due to it not living up to the quality standards of her and a lack of readership. While she left the comic up, she pulled almost all the links to it from all her other comic sites.
Dan Shive shows a lot of remorse for the quality of the early EGS comics. Since he started adding rants to old comics, this came especially clear. For example, he deniesthecanonicality of some characters from an older high school newspaper comic of his in the EGS universe. He also shows regret creating Susan as Straw Feminist (she got better).