Weave Desktop !!top!! 〈Certified〉
Recommended with caveats. Try the free trial first, and be prepared to change your note-taking habits.
Weave runs on your machine, not a cloud server. Files are saved in a simple, open format (JSON + assets). This makes it blazing fast and privacy-respecting. Syncing is your responsibility (via Dropbox, Syncthing, or git), which some will love, others hate. weave desktop
You can color-code nodes, group them with freehand shapes, and add tags. The “focus mode” temporarily hides everything outside a selected group—great for large canvases. Recommended with caveats