vym - VYM (View Your Mind) is a tool to generate and manipulate maps which show your thoughts.
asciiflow - Infinite ASCII diagrams, save to Google Drive, resize, freeform draw, and export straight to text/html.
Freeplane - Freeplane is a powerful and free software for building mind maps.
PabloDraw - PabloDraw is an Ansi/Ascii text and RIPscrip vector graphic art editor/viewer with multi-user capabilities.
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.
JavE - JavE (Java Ascii Versatile Editor) is a free Ascii Editor.