The envelopes of each size are stored in plastic drawers that have been manufactured in the correct size, and the drawers then are stored on shelves that have been spaced correctly for each size drawer. The envelopes are placed into the appropriate size drawer, in numerical order, with the newest item in front. This results in a storage system that has great capacity and is easily managed. Since all bar-codes are on the outside, inventory is a simple matter of running the portable bar code reader wand over each envelope. We also store narcotics and currency in the same manner, using envelopes that have been pre-printed especially for those types of evidence.
Manila envelopes are inexpensive, and are available from any stationery supplier.
I don't know of any commercially available drawers made for this purpose. Ours were custom made by a local plastics manufacturing firm. They are a little pricey, but you only need to buy them once. In lieu of custom drawers, you could store the envelopes in plastic bins from a variety store, or even cardboard boxes that your copy paper is delivered in. With care the containers will last almost forever.