I'm midway through an "organizing" project. Here's what I've done so far. First, I took every fly out of every box I have and separated them into 3 categories: Dry, nymph/wets, and streamer/terrestrial. Next, I bought several Plano model 3701 plastic boxes and began the process of putting flies into their respective Plano box in some semblance of an order. I needed 5 Plano boxes for my collection of flies (I could have made done with 3 if I crammed more into each compartment). These Plano boxes make it really easy to visualize what you've got and they are stackable. They are low profile and have up to 35 compartments per box. Dividers can be removed to allow for bigger streamers and such.

The next step for me is to choose flies from each box to assemble an appropriate mix in a smaller box for whichever waters I fish. All 5 Plano boxes can all be packed into a carry bag should I choose to take them all on a trip, but I'm trying to avoid that. While this plan may not work as well as I'm hoping, it at least forced me to take an inventory of flies I've collected over the years and will probably keep me from buying more stuff I already have!