Plot Factory - Online story planner, organizer, and writing application.
Linked Ideas - A macOS/iOS apps to treat ideas as links of concepts.
World Anvil - World Anvil is a worldbuilding tool for Authors, Storytellers and worldbuilding lovers.
Xmind - Xmind is a brainstorming and mind mapping application.
Scrivener - Scrivener is a content-generation tool for composing and structuring documents.
vym - VYM (View Your Mind) is a tool to generate and manipulate maps which show your thoughts.