Freeplane - Freeplane is a powerful and free software for building mind maps.
Scrivener - Scrivener is a content-generation tool for composing and structuring documents.
Linked Ideas - A macOS/iOS apps to treat ideas as links of concepts.
Final Draft - Use your creative energy to focus on the content; let Final Draft take care of the style.
vym - VYM (View Your Mind) is a tool to generate and manipulate maps which show your thoughts.
yWriter - Free writing software designed by the author of the Hal Spacejock and Hal Junior series. yWriter6 helps you write a book by organising chapters, scenes, characters and locations in an easy-to-use interface.