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.
Celtx - Celtx is a scriptwriting software platform with applications in a wide range of mediums but that specializes in helping screenwriters.
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.
Trelby - The free, multiplatform, feature-rich screenwriting program!