Comment by fragmede
This is not an endorsement of the work, but there's Harry Potter and the Methods of Rationality. I hear 50 Shades of Gray is another fanfic that went mainstream.
A book nerd could come up with a much longer list, but I know there's a ton more illegal unlicensed! Harry Potter fan fic.
50 Shades is decidedly not a fanfic for the exact reason that it couldn't be sold as one.