When I first started sewing, I would print the pdf patterns I was using and throw them away after each use. BUT then I found I was printing the same ones over and over- plus, it is hard to keep track of where they are all stored online.
Then I started keeping them. I kept them in a pile, then I kept them in manila folders by type. This also got messy, especially since some patterns require more than one sheet of paper.
My solution has been binders with plastic sheet covers and making my own dividers with write-on tabs.
What I have done is sort the patterns by category; for example, bags, baby patterns, child patterns, and adult patterns. Each pattern gets its own sheet protector. If I have the same pattern in more than one size, then each size gets its own protector (most of mine are organized this way- I rarely buy standard non-pdf patterns).
Within the binders, they are organized by type; for example, pants or underwear or diapers. I have made labels for each of these types using a sharpie on a write-on tab.
I have found this system far better than anything I have come up with previously. Another idea of an improvement would be to have binders by type (diapers, pants, bags, etc.) then tabs by size (infant, baby, toddler, adult, etc.).