I love playing Dominion, but the boxes the game (and its six expansions) come in take up a ton of space. I'd looked at several other Dominion storage solutions online, but I wanted something that would be easy to pick up and take to game night at a friends, take up less space than the boxes, look good, and protect my cards, without making it difficult to find individual cards. Needless to say, my wife was onboard with all of these objectives.
Luckily, I was able to find off-the-shelf parts for everything I needed. I found clear plastic baseball card cases ($15) at the Container Store that fit Dominion cards perfectly (they're $1.50 cheaper at Amazon). The included clear plastic dividers make it easy to keep expansions separate, as well as make areas for mats, tokens, and the other accoutrements of the game, but they're too thick to use to separate the hundreds of individual kingdom cards. I wanted to find some thin plastic separators to use as dividers, but I wasn't able to find anything that was exactly the right size. The closest I came were these white plastic separators ($25 for 250)--they're the right height, but they're too wide to fit in the plastic tray on their side.
I needed to trim about 3/8ths of an inch off of the square edge of the separators for them to fit properly, so I invested in a paper trimmer that would help me measure accurately and keep the edges straight. I ended up buying a Fiskars model that's no longer in production, but the mechanism is the same as this model ($20). Cutting through the thick plastic required a fair amount of force on the mechanism with the sliding blade, so don't be afraid to push. You'll need a separator for each different card in your collection, so you'll be making quite a few of these--I needed to cut several hundred.
Once you've cut your dividers and made sure they'll fit in the trays, you'll want to attach some sort of label to each divider. I just used the labels that came on the insert for each expansion's box. It was simple to cut the labels out of the insert using the paper trimmer, but you could make (or print) your own, if you don't want to destroy the inserts. To affix the labels to the dividers, I bought a Scotch Adhesive Dot roller ($6). Make sure you apply the glue to the back of the labels, not the separator cards--you don't want the cards sticking to each other. I found that the labels looked best if I oriented the separator cards so the square edges are on the left and affixed the labels to the top-left corner of each separator. Don't forget, you'll need labels for base cards and randomizer decks too.
After a lengthy conversation with my wife, we decided to keep our cards alphabetized by expansion. Each tray holds two expansions without base cards (Alchemy, Hinterlands, Cornucopia, and Prosperity), or one expansion with base cards (original Dominion and Intrigue). We put all of the mats, tokens, coins, and other items that come with all the expansions into the back of the tray containing Seaside. I should probably make some attractive labels for the front of the trays, but I haven't found them necessary yet.
The only downside to using trays is that the instructions don't fit in these boxes. So we can easily look up rules clarifications and the like, I downloaded the instructions for each expansion in PDF for from Rio Grande's site and put them in a Dropbox folder, which either of us can access from an iPad, laptop, or phone.
All told, our Dominion games take up about half the space they did before and the game is much more portable if we want to bring it to a friend's house. Best of all, having quick accessibility to all the cards means it's much easier to play games with all the expansions mixed up and has brought new life to our Dominion play.
I haven't done it yet, but there's no reason this wouldn't work for any deck-building games--Thunderstone, Nightfall, Penny Arcade: Gamers vs. Evil, or any other games that use Dominion-sized cards.