Contrary to OPs opinion, I believe tooling is relevant to the learning process, because an inconvenient system will put you off from taking notes and from coming back to them in the future. The catch is, there is no single tool that will fit everyone, you have to find your own method. My own tooling choices have changed a lot across the years.
When I began to apply a structured method to my studies, my first choice was to use mind maps. You can structure a mind map to resemble the associations you have in your own (duh) mental model of any body of knowledge you might be studying, and then it's easy to navigate a map with your eyes to recall stuff and fill the gaps when things get cloudy in your head. The first digital tool I recall using was CmapTools, and it's still pretty good.
Nowadays I use mostly LiquidText for reading notes, on books and articles (but there are other similar products). It lets you build something similar to a mind map, and it's really convenient to select a piece of text or image on a pdf and make it a node in a map. It's especially convenient if you have an iPad Pro with a Pencil. However, I could still not find any single tool that encompasses all my "learning modes". For instance, if I am playing with some OSS project and want to take note on something interesting, I have to use a different product.
When I began to apply a structured method to my studies, my first choice was to use mind maps. You can structure a mind map to resemble the associations you have in your own (duh) mental model of any body of knowledge you might be studying, and then it's easy to navigate a map with your eyes to recall stuff and fill the gaps when things get cloudy in your head. The first digital tool I recall using was CmapTools, and it's still pretty good.
Nowadays I use mostly LiquidText for reading notes, on books and articles (but there are other similar products). It lets you build something similar to a mind map, and it's really convenient to select a piece of text or image on a pdf and make it a node in a map. It's especially convenient if you have an iPad Pro with a Pencil. However, I could still not find any single tool that encompasses all my "learning modes". For instance, if I am playing with some OSS project and want to take note on something interesting, I have to use a different product.