I didn't organize my patterns until fairly recently. At last count I have over 800 patterns. Its a lot, but it definitely doesn't put me in the category of "great pattern stashers of the 20th century". I store my patterns in cardboard boxes; some bought for that purpose, some are old computer-paper boxes. My sister, whose pattern stash is much larger, prefers to keep hers in filing cabinets.

When I get a new pattern I remove the envelope contents and place them in a 7-1/2" x 10-1/2" clasp envelope. In marker I write the pattern company, the pattern number, a brief description of the pattern, and the size(s). I then file the pattern in the correct box, sorted by pattern company then by number. The same way you find them at the fabric store.

I then iron the envelope (to make it lay flat) and add it to my pattern book. I can get two envelopes into a clear plastic sheet protector (one facing front and one back). These are in 3-ring binders sorted by pattern type. I considered photocopying the covers, but I find putting the envelope itself in the bider saves time, money and paper.