Logseq

Logseq is for people who think in bullet points and want their notes to reflect how their brain actually works. The outliner format means every note starts as a bullet, and the daily journal workflow encourages you to write first and organize later. The bidirectional linking means ideas connect organically as you write. The PDF annotation feature lets you highlight text in a PDF and turn those highlights into linked notes in your knowledge graph. The flashcard system built into the app means you can turn notes into study material without leaving the app. It is fully open source with AGPL licensing. The trade-off is that the outliner format is not for everyone — if you prefer long-form writing, Obsidian or Joplin might suit you better.

Best for users who are comfortable following setup instructions or running a self-hosted tool.