Others before me have had good ideas for pattern storage. Here's one more that works great for me:
Sterilite Legal/Letter File Boxes cost $6.97 at Walmart and are located in the office supply area of the store--not by all the other storage bins. These bins hold 2 rows of sewing patterns perfectly. And the larger size patterns like Jalie, Style Arc or downloadable patterns fit perfectly too if they are turned sideways. You can see pictures of them here I have six bins all organized by category and company name, and patterns are in numbered order. It is so nice to be able to locate a pattern quickly.
The boxes have flat lids so stack nicely. The lid is made so the bottom of one box fits in a ridge around the edge of the lid which is good because you won't ever cave in or crack a lid due to the weight of bins stacked on each other. And with the flat lid they can be stored nicely on a shelf too. I have over 80 patterns in the bins pictured and still have wiggle room to look through the patterns. The sides of these boxes are straight up as opposed to the sloping sides of regular storage bins, so I think that's why they work so well for patterns. Also, there is a comfortable molded in handle beneath the two lengthwise top edges.
Unfortunately, the bins are not available for home delivery. They can only be bought online and picked up at the store or simply bought at a Walmart store. However, I feel sure the same size clear Legal/Letter File boxes could be found at any office supply store too. They really are the perfect size for patterns but just make sure you are buying the 'Legal' Letter size file box, not the regular size letter file box.
Update on 11-12-12:
I was at 2 different Walmarts lately. The legal letter file bins I bought from Walmart and use are clear with black lids. I've now noticed they sometimes have a smokey color too. But just in case Walmart stops carrying them altogether be sure to look at any office supply store. With a quick search I found these at Staples