Trilium Notes is a hierarchical note taking application with focus on building large personal knowledge bases.

Logseq is a privacy-first, open-source knowledge base that works on top of local plain-text Markdown and Org-mode files. Use it to write, organize and share your thoughts, keep your to-do list, and build your own digital garden.

https://github.com/logseq/logseq

Automad is free to use and open-source.

https://github.com/marcantondahmen/automad