I put the patterns in sheet protectors and then file in 3-ring binders. When I first started quilting (about 15 years ago), I only had a couple of binders. Now I have a binder for every category (ie: purses, totebags, etc.) It is so much easier to find the patterns I am looking for this way. Some binders are small - 1" wide others are 2-3" wide. Every couple of years I go through my binders and get rid of the patterns I no longer want.
I do this for all my patterns - whether they came out of a magazine, freebie on the internet, or something I purchased.