With a separate notebook in the following format:

pagenr:linenr - note

Here’s my answer:

At some point before or during reading, I copy the table of contents of the book so that it’s easy to search for. It’s often enough for internal links, too.

While reading, I usually take a picture of the page and insert it (then, when I’ll process them, I’ll write the actually relevant part in my own words, so I don’t bother transcribing). I can also write comments under the photo if needed. This is my usual way to go, especially for books from the library since I won’t be able to quickly check them if I’m unsure of something.

Sometimes I’ll also just write the page number, which effectively forces me to go back and read the entire page and figure out what was so interesting in there. It’s super efficient to keep things simple and make sure I don’t confuse something that strikes me and something that’s actually worth remembering!

In both cases though you need a processing step (personally, I do that in Obsidian). I think we should always have one, but it’s something to keep in mind :)

Maybe use sticky notes and once you finish your book you can rercreate them with a digital tool.