Pretty standard stuff for me. I have six fly boxes now, all small enough to fit at least four into my vest. Since I tie probably 75% of my own flies, I usually only carry 6-12 of each specific pattern at any one time unless I am going on a long trip.
2. Mayfly and Caddis nymphs
6. Lake or species specific
Insie they are organized by pattern and size. I am kind of a boy scout when it comes to organizing all my fly fishing gear.
Here's a "trout only " answer from a person who fishes mostly trout.
Dries on the left; by the season (little black stones, blue quills, hendricksons/red quills, quill gordons, march browns, sulfurs, green drakes, slate drakes, yellow sallies, caddis, attractors (humpies, wulffs, stims). Soft hackles at the bottom on the left side (partridge and almost anything, Leisenring/Hiddy patterns).
Nymphs on the right (pheasant tails, hare's ears, princes, chironomids, worm patterns). Small selection of terrestrials (ants, chernobyl ants, hoppers, crickets), buggers/streamers at the bottom on the right side.
I am of the species specific mode for my boxes...Steelies I have my nymph box and my egg box and a box for streamers. For stream trout, I do the same, dry box and wet box. For my Hex fishing at night, hex patterns and a few mice thrown in. Smallies pretty much the same program... But in all my boxes I may have a few of the other type; just in case...lol
I have my Alaska boxes, San Juan boxes, Saltwater boxes, Bass box and a dry fly box. I generally carry the flies I plan to use for the day in one or two small boxes. My San Juan boxes should really be called my Tail-water boxes.
Big: streamers, buggers, muddlers, poppers, taratulas. (This doubles as my smallmouth box.) Medium: Mix of dries, wets, terrestrials, and nymphs size 10-16. This is typically the only back country box I'll carry though I might throw in a few buggers. Small: Midges and tiny dries. Keep em handy for tail-water and clear water solutions.
I have one extra 16 compartment double side fly box, that is strictly for reloading and doesn't go to the water. Dries in compartments and others on felt.
My problem is taking too many flies, and this set-up limits me a little.
I "organize" them by type. I use boxes with ripple foam on one side and flat on the other. On the foam, I start at the "top" of the box with dries, and after I got 'em in the box I go on to wets, then nymphs. On the flat side I start at the "bottom" and put the flies in by type so that the eyes of the hooks on the ripple side are facing the opposite direction of the ones on the flat side. Then I start off with streamers, and sort them by type, Bucktails, Buggers, Featherwings, Marabou, ect. Then I toss the rest in at the bottom. The rest includes bass bugs, poppers,ect.
I usually organize them by type, then by size. Grouping things together: streamers, tricos, midges, etc. The only exception is my terrestrials. I have a few in each box, usually in the lid. They are larger than most anything else I carry and my Morel boxes are not the largest. But, I try to keep the same types together like ants, hoppers, crickets....
Do the little plastic cups from the fly shops count? Just throw them all in there and call it good! He he. 2 boxes for nymphs, one box for dries, small box for wet flies, a midge box and one for streamers.