Trilium

AFFiNE brings documents, an edgeless whiteboard, databases, knowledge management, and planning into one workspace. Rich text, notes, web embeds, linked pages, shapes, and slides can coexist on the same canvas, while local-first storage is paired with cross-platform synchronization and real-time collaboration. The Community Edition can be self-hosted, and optional AI features can turn material into reports, slides, mind maps, or plans. It suits people who want fewer boundaries between note-taking and visual thinking.

SiYuan organizes personal knowledge around content blocks, bidirectional links, and a WYSIWYG Markdown editor, allowing references, queries, PDF annotations, and tasks to live in one workspace. It offers desktop and mobile apps, can be self-hosted with Docker, and exports to formats including Markdown, PDF, Word, and HTML for users who want stronger control over their data.

Logseq combines Markdown or Org-mode notes, bidirectional links, and a knowledge graph for organizing ideas, tasks, and research. It also supports PDF annotation and an ecosystem of plugins and themes across desktop and mobile clients. Its newer database graphs are in beta, while real-time collaboration and the new mobile app remain alpha features, so important data should be backed up before adopting them.

Tolaria is a desktop app for organizing personal notes, company documentation, or agent memory on macOS, Windows, and Linux. Notes remain standard Markdown files with YAML frontmatter, and every vault is a Git repository with portable version history. It works without a Tolaria account, subscription, or cloud backend, so the knowledge base remains usable in other tools.