The only thing I've really found that I like is a plano box for spey flies. I know that sounds crazy - but I really only use about 5 different flies.... ok maybe 8. I just put them in the container slots.

I've also been using a lot of tube patters that fit nicely in the plano containers as well. Something like this but without the smaller compartments.
http://www.marinegeneral.com/images/productimages/plano-3449-87.jpg