As you might imagine if you saw the frightening state of my sewing space, I have "a few" patterns scattered about. While it's tempting to just stash them in a box to get them out of the way, I decided I might as well do it right.
Maybe it's just me, but I find most pattern envelopes to be terribly inadequate. They're flimsily made and once the pattern has been taken out and used, trying to fit it back into the envelope is nearly impossible in the absence of mad origami skillz.
My solution (yes, I have a system; the issue is to "use it.") is to store patterns in 9" X 12" catalog envelopes. Each pattern has it's own catalog envelope. I cut the orginal envelope apart. The front of the original envelope is pasted onto the front of the catalog envelope; the back of the original envelope goes inside with the pattern pieces and instructions. The envelopes are stored in banker's boxes, filed by pattern number without regard to manufacturer.
Catalog envelopes open on the short end of the envelope, unlike booklet envelopes which open along the top. Banker's boxes are sturdy, cardboard boxes that come in either standard or legal size with a variety of closure options (I like the kind that have separate lids). Both catalog envelopes and banker's boxes are available at office supply stores such as Office Max or Staples.
Three reasons why this works well for me. (1) The catalog envelopes fit perfectly in a standard banker's box. (2) After using a pattern, I don't have to spend hours refolding the pieces so that they'll fit into the original envelope. (3) When I want to buy fabric for a particular pattern, the yardage requirements (the back of the envelope) are ready to go with me.