I built myself a new box for Dominion. I found the plans in Geek, but had to fix them a bit — for one, the suggested length of 285 mm is huge, my box is slightly too short at 210 mm, correct length with Ultra Pro soft sleeves should be something like 230 mm to fit in Black Market and Envoy.
Here’s a comparison with the Intrigue box. I can’t fit both basic Dominion and Intrigue in my backpack, but two of these small boxes — no problem.
Here’s a closeup, so you can see the simple dividers in the boxes. The cards are all sorted in alphabetical orders, but with the score and money cards in the beginning, since they’ll be used always.