Begin with portable words
Plain text and Markdown files can be opened by many tools. A descriptive filename and a title at the top of each note are enough to make a useful beginning. Tags and links can be added later. First make sure that every note makes sense on its own, without depending on one app to explain where it belongs.
Leave context for your future self
A saved link says little about why it mattered. Write down the question you were trying to answer, what you learned, and what remains uncertain. One or two sentences in your own words can save a full afternoon of rediscovery months later. The best notes are not transcripts of everything you read; they are signposts back to your thinking.
Export before you need to
Even a favorite service may change its prices, features, or export format. Keep a periodic copy of your notes in a format you can open elsewhere. Try a few random files after each export. Portability is not a promise printed on a settings page; it is a small test you can perform yourself.