vym - VYM (View Your Mind) is a tool to generate and manipulate maps which show your thoughts.
MediaWiki - MediaWiki is a free software wiki package written in PHP, originally for use on Wikipedia.
Linked Ideas - A macOS/iOS apps to treat ideas as links of concepts.
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