Manuskript - Open-source tool for writers.
vym - VYM (View Your Mind) is a tool to generate and manipulate maps which show your thoughts.
StoryMill - Developers and publishers of Mac, Win, and iOS productivity, home and office and writing software such as MacGourmet, Paperless and many more. Based in MN.
Freeplane - Freeplane is a powerful and free software for building mind maps.
BlankPage - Stay motivated to write, and finish your story
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.