Freeplane - Freeplane is a powerful and free software for building mind maps.
Workflowy - A better way to organize your mind.
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.
Orgzly - Outliner for notes, tasks and to-dos
vym - VYM (View Your Mind) is a tool to generate and manipulate maps which show your thoughts.
UV Outliner - UV Outliner is a small and powerful single-pane outliner.