SiYuan

SiYuan treats a note like a collection of blocks. You can refer not only to an entire document, but also to one paragraph, list or other part. For example, if you link study notes to a project, you don't have to retype the same explanation over and over again.

The editor combines Markdown input with direct formatting. You also use tables, mathematical formulas, diagrams and references to PDF notes. This makes SiYuan useful for extensive personal reference work, but requires more furnishing than a simple notepad. Start with a few notebooks and expand your structure as soon as you notice what information you often seek back.

Your documents are in a workbook in its own .sy format, along with attachments and other parts. For use outside SiYuan, you can export to Markdown. Most functions are free of charge; for certain additional services a paid membership is required. So check out which synchronization form suits your devices and budget.