Scrivener

Scrivener is a word processor for Mac OS X and Windows intended for writers (professional or amateur), allowing the maintenance of notes and annotations in addition to the main document.

Projects are stored in a directory structure, using the .scriv extension in the name. (In Mac OS X, such directories are treated by the Finder as a single file, obscuring their internal structure, but in Windows they act like normal directories.) The directory and its sub-directories contain RTF (Rich Text Format) documents, HTML files, various XML files and possibly all kinds of files added to the research folder of the project (e.g. PDF documents, pictures, videos, sound files, etc).