Funny. I was just blogging about this. Here is where I am and what my thinking was
Here is the what:
Scientific anglers clear waterproof boxes
These were too small and too bulky. For the volume they took up they didn't hold a lot of flies. I ended up with 1 of 5 different types. I GAVE all of them away. And they were HEAVY.
CF DESIGNS large water proof boxes
C&F Fly Box - C&F Fly Tying » C&F Design
I bought 2 of the large waterproof fly boxes that allow inserts. I purchased about 15 inserts and had those in a separate plastic bin as storage. You just make up a bunch of insert/sheets and then drop them in as needed. Brilliant.
I decided to go with 2 Wheatley boxes for trout fishing. I picked up a used green one on ebay and will be getting a similar black one new. I'll setup one up for wet and one for dry. I like doing that.
I also have a big Montana Fly Box company boat box with an extra leaf page. It holds tons and I fill that when I'm riding along in a bass boat.
Here is the why:
Bulky deep boxes, while they can hold big flies without crushing them are often too thick taking up precious room in chest packs or jacket packets. This makes stripping line awkward. They also rob space in sling packs.
These days plastic is EVERYWHERE. The CF design boxes are heavy but deep so I use those primarily for bass fishing when I'm typically on a bass boat or in a kayak where I have way more room and not lugging boxes around.
The Wheatley's are aluminum and not as thick. They are my boxes for trout where I have way more types of flies (wet, dries, terrestrials, streamers, nymphs) and need the benefit of compartments.
Storage ability and organization
CF boxes hold a lot but I think the Wheatleys store nearly as much and with more potential to stay organized.
Probably a small consideration but since I only carry 2 boxes I go with different colors for quick identification.
Eh. I splurged on the CF boxes partly because of the waterproof feature. I don't think it was worth it. I thought dry flies will dry. I don't fish in the rain much. I won't put a cell phone in there. And yeah, it might keep the box afloat if I drop it. But, I dropped the Wheatley box yesterday and it floated long enough for me to grab it.
For fly storage at home. I use a Plano chest that stores all of the inserts in the top portion as well as boxes. Then drop all the extra flies in the bins below. It allows me to quickly move all my flies to a car if I'm going on a multi-day driving trip with a stay in hotel/cabin.