SiYuan

SiYuan is a block-based note-taking and personal knowledge base where every paragraph is an addressable block you can link and reference. It offers a WYSIWYG editor with block references and backlinks, a graph view, flash notes, templates and a large plugin API, and it can run as a self-hosted server so the data sits on your disk.

Researchers, writers and engineers use it to build connected notes, keep a daily log, and outline longer documents without losing the source of a claim.

Keeping it on your own server means the notes never leave the machine, there is no per-seat fee, and the workspace directory is straightforward to back up.