I have a couple of favorite designers where I keep all of their patterns together. Example: Terry Atkinson Designs are all stored in plastic sleeves in one 3-ring binder. Bonnie Hunter's designs are all in another 3-ring binder.
At this stage of my craft I find my interests fall in specific areas: history, contemporary, traditional and misc. I treated myself to four nice decorative storage boxes with removable lids. Magazine articles are removed from the publication, stapled together and placed in these storage boxes. I don't (repeat don't) want to spend so much time organizing that my actual sewing time is gone!!!! I do want the information readily accessible and stored neatly. :-)
My shelves are filled with books and 3-ring binders. Some of the soft-cover publications have been hole-punched at a local printer's shop. That investment has helped me keep all of Mary Ellen Hopkins priceless books together neatly, as an example.
Books I have little interest in and used magazines can go to the free pile at guild meetings. Good Luck!