In Homestar Runner, there's "Marshmallow's Last Stand", the very first cartoon featured on the website. Once the quality of the shorts began to noticeably improve, the Brother Chaps removed "Stand" from the live version of the website and moved it to the museum (the area of the website where they archive old stuff for historical purposes), and then later removed it from the museum as well. Their reason: "The characters are completely different. Saying and doing things they'd never do now."
Egoraptor has said that when he posted the first episode of Metal Gear Awesome on Newgrounds, he thought it would get blammed (deleted for sucking).
Jonathan Ian Mathers of Ill Will Press, producer of Neurotically Yours has, for quite some time, consistently denounced and attempted to suppress much of his earliest work; typically citing the heavily Fanservice-oriented nature of it. However, much of his more recent work pushes the fanservice envelope much farther; the only difference being that it's now done "ironically" instead of straight.
Subverted with Chakra-X with his Sonic the Hedgehog Fan animation Nazo Unleashed. Despite the use of rotoscoping off certain scenes from the likes of Sonic X and Dragon Ball which he considers lazy and crude, he says he's still proud of it in the Hd directors cut, stating that he considers it a milestone in his animation projects, and uses the movie as a benchmark for his future original projects.