I have also not found a great way to take notes while reading books, but most of my reading is on my computer right now. That makes digital note taking the obvious choice, and space isn't really an issue in that case. My way of deciding what to take notes on is by simply asking myself: could I want to remember this in the future? If the answer is yes (it usually is if I even considered asking it) I make a note of it. The note minimally contains a reference to the source, and some links to related topics. The links to related topics allows me to discover the note in the future by referencing the backlinks on those topics.
I recommend looking into the Zettelkasten method for note taking, if you are not already familiar. It is originally used with index cards, so you might find it to be a useful way to handle taking notes on index cards. I use a Zettelkasten-inspired digital note taking system called Org Roam. The thing I like the most about Zettelkasten is that it minimizes the effort for getting your ideas out of your head. You can worry about organizing the ideas after you have them laid out in front of you.
I use Obsidian at work to organize and plan. When looking up ways to effectively use that I stumbled down the Zettelkasten rabbit hole. It’s a little too involved for my needs. It seems like it might be good if I was doing research to write a book, but is too involved for my daily life. I can see where taking and organizing the notes would turn into a hobby, which is enough of a problem for me already.
I’ve considered reading on the computer, maybe I should actually give it a try.
> I’ve considered reading on the computer, maybe I should actually give it a try.
I should note that I haven't actually gotten into a workflow where I read ebooks and take notes. Most of the reading I do is documentation for systems I program with. I take tons of notes on documentation so I can easily find what I need again in the future.
I recommend looking into the Zettelkasten method for note taking, if you are not already familiar. It is originally used with index cards, so you might find it to be a useful way to handle taking notes on index cards. I use a Zettelkasten-inspired digital note taking system called Org Roam. The thing I like the most about Zettelkasten is that it minimizes the effort for getting your ideas out of your head. You can worry about organizing the ideas after you have them laid out in front of you.