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MediaWiki - MediaWiki is a free software wiki package written in PHP, originally for use on Wikipedia.
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.
Confluence - Confluence is content collaboration software that changes how modern teams work
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.