Before you start taking notes, ask yourself what your goal is.
Paper versus digital. If your goal is to study the content of a book, paper is better. But if your goal is to be able to reference certain parts of the book easily, an ebook may be better suited.
Serendipity versus control. When you want to take notes to read them for pleasure afterwards, highlighting and marginalia could be more suited. But if rediscovery is your desire, a structured system, such as an index of the key ideas, may be better.
Learning versus creating. If you want to learn from a book, your notes will be factual, but if you're going to create your own content, your notes will be more original.
Taking notes should not become a tedious process, but it should be made as seamless as possible.
If you are reading a physical book, write down main ideas or questions in the margins. Try to keep it very short. If you are reading an ebook, highlight the essential parts and write a few words to add contextual information.
If your goal is to learn or reference your notes in the future, you may want to stop at the end of each chapter and collate the ideas separately from the text. This can be done on the inside cover of the book, or on a separate index card, where you rewrite the key ideas with the corresponding page numbers.
Learning how to learn: how to make your ROI on reading explode Learning is a heavily misunderstood concept. As a paradigm example of deep work, we understand that, when reading, directing your full attention to the material at hand is essential. Grasping complex information is hard. But this is only half the battle.