Scrivener - Scrivener is a content-generation tool for composing and structuring documents.
SuperNotecard - Introducing SuperNotecard. SuperNotecard is an online writing tool that features virtual notecards to help arrange facts or scenes, track details, organize paragraphs, and clarify your composition process.
Manuskript - Open-source tool for writers.
vym - VYM (View Your Mind) is a tool to generate and manipulate maps which show your thoughts.
DocxManager - DocxManager is an elegant tool for writers that are requiring any management work for the word.
Freeplane - Freeplane is a powerful and free software for building mind maps.