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Libre office draw is wonderful, it can edit pdf docs at ease. It’s crazly powerful compared to paint 3d
Freeplane - Freeplane is a powerful and free software for building mind maps.
draw.io - Online diagramming application
Linked Ideas - A macOS/iOS apps to treat ideas as links of concepts.
yEd - yEd is a free desktop application to quickly create, import, edit, and automatically arrange diagrams. It runs on Windows, Mac OS X, and Unix/Linux.
SuperNotecard - Introducing SuperNotecard. SuperNotecard is an online writing tool that features virtual notecards to help arrange facts or scenes, track details, organize paragraphs, and clarify your composition process.
Dia - Dia is a GTK+ based diagram creation program for GNU/Linux, MacOS X, Unix, and Windows, and is released under the GPL license.