Freeplane - Freeplane is a powerful and free software for building mind maps.
OmniOutliner - OmniOutliner is a writing app for collecting information, outlining ideas, adding structure to any sort of writing.
Linked Ideas - A macOS/iOS apps to treat ideas as links of concepts.
Dynalist - Dynalist is a web app that lets you break down and organize your thoughts in the format of lists.
vym - VYM (View Your Mind) is a tool to generate and manipulate maps which show your thoughts.
Outlinely - Indispensable information organization tool for knowledge workers.