A good number of the books I've read and kept for future reference, I'm only interested in a few pages, and then it's just some information on those pages that's needed, and that info is not formulated as well as it could be: it would benefit from a rewrite. It's possible to improve on the source material i.e. to make it more concise or more memorable or to expand upon a concept that's been written about in the text, or to make links with concepts in other texts. For books like that, it's been worth making notes on a word processor, with details of the source material (with page numbers in case I need to look it up in future). For that I use .docx files in thematically titled folders. (I guess I could add tags in the file metadata so that those files become searchable.) The notes on each book can be as short or long as the book merits.
I guess I end up with a searchable annotated catalogue of the contents of my bookshelves, with the advantage that I can refer to the relevant pages in those books in future without having to pore over whole books to remember their contents when I want to look up something specific. The system encourages me to actually (skim) read the books I've got which in turn prompts me to discard those that are not worth keeping - a number of them will be out of date or just a bit rubbish.