I use Myran fly boxes for my hooks. The 18 compartment box is 6 1/2" x 4" and is capable of storing approx 3600+ hooks dependant on sizes. I use mainly 12-18s and could put 2-300 in each of the 18 compartments.
Two boxes, one for nymphs and one for drys is more than enough storage for me. The boxes are very tough with solid hinges and close firmly. 6.50 each-cheap as chips. Mine come from Ted Carter fishing supplies (google). The little yellow thingy in the 1st pic has a magnet at one end, handy for easy hook removal. Hth.
Chris.