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.
Freeplane - Freeplane is a powerful and free software for building mind maps.
OneNote - Get the OneNote app for free on your tablet, phone, and computer, so you can capture your ideas and to-do lists in one place wherever you are. Or try OneNote with Office for free.
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
vym - VYM (View Your Mind) is a tool to generate and manipulate maps which show your thoughts.