When I buy a new pattern, I make a copy of the envelope front and back. If it's a PDF, I print out the cover/line drawing and yardage info page. If one pattern comes with different types of garment (e.g. top and skirt), I make multiple copies.
The printed/copied page then goes into my pattern catalog binder. The binder is divided into types of garment: top, skirt, pants, dress, outer, underwear, and bag.
The unused physical pattern envelopes are stored in a box in alphabetical order by company.
Once the pattern is used, I put them in a manila envelope so that I can keep original patterns and traced patterns together and keep the instruction and pattern pieces from PDF patterns together. I write down the pattern company name, pattern # or pattern name, and a short description of the pattern ("McCalls 7254" then below it "cardigans") at the right top corner of the envelope and right side edge of the envelope. The envelopes are then stored in alphabetical order by company.