I do it by techniques, subjects, interest and author. All my color books are together, hand and machine stitching, applique, etc.
When I'm reading a new book, I keep a pad of multi colored sticky markers and try to use the same color for things of interest. Projects are red, techniques yellow, tips green or what ever. I've also seen others suggest keeping a sheet of paper on the front of magazines with the projects of interest listed or indicated if you copy the table of contents.
Mine are not nearly as organized as I'd like them to be. They are in my bookcases, on top of my dressers and on top of our bed headboard. I keep thinking I need to cull...