At the moment I just have the base set of Dominion and Dominion-Intrigue, each of which are a full set so currently I'm storing each per the in-the-box organizers in their original boxes.
But when we buy another expansion (and more after that) I'm starting to wonder how we can best store all of these expansions. I've seen (but don't recall exactly where) various solutions for storing Dominion cards.
For us I think the following features would be needed:
easy and rapid setup (so no need to resort piles beyond counting out the numbers of some cards per the number of players - which in our case is usually two)
easy to clean up when the game is over and/or set up another game with a different set of cards
consistency in how the cards are organized - I've noticed that the default organization structure changed between the Base set's layout and Intrigue (the base set alpha sorted while Intrigue sorted the cards into more categories before alpha sorting)
Ideally space efficient so we can more easily travel with our games