TiddlyWiki - a non-linear personal web notebook
Freeplane - Freeplane is a powerful and free software for building mind maps.
wikidPad - wikidPad is an application for storing thoughts, ideas, todo lists, contacts, or anything else that user can think of to write down.
Linked Ideas - A macOS/iOS apps to treat ideas as links of concepts.
Knowledge Workshop - Learning Management Solutions provides innovative and reliable software for the knowledge worker.
vym - VYM (View Your Mind) is a tool to generate and manipulate maps which show your thoughts.