I used to take notes on books in notebooks and mark the page numbers. Over time it switched to ebooks with TextEdit, then org-mode for writing thoughts on books/talks. It's nice to break a book down by section or concepts and have it all in one place as opposed to being scattered throughout random pages or listed at the end of the book.
It's usually pretty easy to convert ebooks/pdfs to audiobooks or use a TTS tool to read each page, one at a time. That makes it easier to write notes while you're listening to the book. You can also get used to reading around 400 wpm, which is nice if you're a slow visual reader.
Since the comments aren't directly in the book, it's not as geared towards English editing as marginalia is. It's great for summarizing technical material though or learning new concepts!