I use the floppy 3 1/2 plastic boxes that carry about 5 disks (50 cents, Office Depot). Just glue foamy sheets on both sides, and there's a great size nymph or midge box that can hold up to 100 flies.
Nestled together, rows on rows,
With their keen, sharp pointed toes,
Here's a Hare's Ear, there a Glory,
A Royal Coach with a wonderous story.
~ H. Wheeler Perce (Fly Box)