I'm not a big fan of a mother ship tackle box. I keep several (and I do mean SEVERAL, as in expanding to fill the universe) boxes for various purposes. For example, bait hooks of many sizes so I always have a hook for the bait I need to use. One for turtle grass northern gulf flats fishing while wading. Another one for bonefish flies. Another one for northern gulf inshore flies. One for local northern pike fishing. It's kind of like golf clubs; pick the right ones for the job and combine them for a particular trip or outing.
I believe that modularizing like that keeps the various applications intellectually manageable, and I always have what I realistically need. For example, I don't likely need #20 midges while fishing for sharks, so I don't have the midge box with me then.
Lots are avaiable, but one I will specifically mention as remarkable is the Plano box that's made for stink baits like Berkley Gulp Alive. It's small enough to fit in a wader pocket or fly fishing vest, and seals positively. It looks like the one at the link below, but dimensions are smaller. I like it in combination with Gulp Alive because the color of the baits doesn't bleed, so I can keep baits like a chartreuse and minnow-colored baits in the same box. I keep an assortment of sizes and colors, and just love that thing. There is NO stink, and I'm comfortable keeping the box in the house or in my car.
http://www.tacklewarehouse.com/Plano_Li ... L3700.html