ConnectedText - ConnectedText is a powerful but simple information management system.
vym - VYM (View Your Mind) is a tool to generate and manipulate maps which show your thoughts.
TiddlyWiki - a non-linear personal web notebook
Freeplane - Freeplane is a powerful and free software for building mind maps.
Zim Wiki - Zim is a graphical text editor used to maintain a collection of wiki pages. Each page can contain links to other pages, simple formatting and images.
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.