Joplin - Joplin is a free, open source note taking and to-do application, which can handle a large number of notes organised into notebooks. The notes are searchable, tagged and modified either from the applications directly or from your own text editor.

Linked Ideas - A macOS/iOS apps to treat ideas as links of concepts.

Standard Notes - A safe place for your notes, thoughts, and life's work

Freeplane - Freeplane is a powerful and free software for building mind maps.

Evernote - Bring your life's work together in one digital workspace. Evernote is the place to collect inspirational ideas, write meaningful words, and move your important projects forward.

vym - VYM (View Your Mind) is a tool to generate and manipulate maps which show your thoughts.