Last year and this year, I’m using a smallish box with slit foam inserts. It has been working really well for me. It was very inexpensive from Fly Tyer’s Dungeon. I just checked his website, says its currently out-of-stock:
http://www.flytyersdungeon.com/Fly%20Fishing/bug_box.htm
All of my fly boxes are relatively thick, heavy tan plastic boxes with ridged foam inserts on one side and a flat foam insert on the other side. I have three sizes. Small which will fit in a shirt pocket. Medium which will fit in a pants pocket (front or back) and large which is a shade too big to slide into any regular clothing pocket. The were four, five and six dollars each respectively from Hook and Hackle back in Bob’s days. I bought a bunch in each size. The foam inserts are getting pretty chewed up from use so I will be using Normand’s tip about making slotted foam insets very soon. Not very glamorous but effective and a shade better then a Ziplock bag. 8T 
pill bottles
I just set up a box for bassin’ as one of my fishing new years resolutions is to put more effort into catching non-trout on the fly. From the looks of this, i’ll be making a twin soon for panfish.
Really simple.
I got a Plano 3640.
Got some of the thicker craft foam I had lying around. 1/4" thick, I think…you could also glue together a few sheets of 2mm tying foam to get about 1/4-3/8" thick foam.
Cut to suit the large compartment on the right side, and adjust the dividers on the left to suit.
I then cut slits in the foam and placed in the compartment, just like a Cliff’s box. I was going to glue it in, but I must have done well in the sizing, and I couldn’t pull it back out to get glue on it! 
I place big streamers in the slits (this is where your poppers would go), smaller, more manageable flies in the compartments. I’ll also be using a few compartments for spooled, flat lead for weight, and a tube of gel floatant, so that I dont need my vest. This is because 90% of my bass and gill fishing is either a 5 minute drive from home and the epitome of light weight fishing…or a grueling day-long canoe trip where i still wont want the added weight of a vest.
The box also has an O-ring to make it waterproof, so it’ll float (for some time, anyhow) if it gets somehow ejected from the boat. I also plan on gluing a pair of Zerust tabs to the sides, lid, or dividers, to prevent hook corrosion, as the flies in this box will get very soggy and will be put away wet.
I use the Plano plastic fly boxes from Wal-Mart. Usually under $5.00.
Bass Bug I did try out your box idea. I made two of them. They are fantastic. The pistol case was cheaper than the foam. But in a pinch you can use regular craft foam instead. It would hold a heck of a lot of bream flies, but it won’t fit in your vest. It makes a great boat box too.
Kel, Glad it worked out for you. They are not small but neither are the flies that size box is designed for. I carry a couple of ‘normal’ size (4x6) fly boxes in my vest, but I usually also carry a small book-bag size day/back pack with my pistol case fly box and other items that wont fit in the vest. (lunch, water bottles, binoculars etc.)
Well, I carry more flies than that what with the wind and those voracious bark skined cottenwood fish. But thats the idea.