Scrivener - Scrivener is a content-generation tool for composing and structuring documents.
Freeplane - Freeplane is a powerful and free software for building mind maps.
Celtx - Celtx is a scriptwriting software platform with applications in a wide range of mediums but that specializes in helping screenwriters.
Linked Ideas - A macOS/iOS apps to treat ideas as links of concepts.
Trelby - The free, multiplatform, feature-rich screenwriting program!
vym - VYM (View Your Mind) is a tool to generate and manipulate maps which show your thoughts.