This is sort of tangential, but I discovered an excellent way to protect the cards during airline or cruise travel, when you don't want to take the original box (or a monster box), due to its dimensions. I put all the cards in a box that a new scuba diving mask came in. These mask boxes are usually clear or semi-translucent plastic, so they are relatively easy for security folks to deal with. The rounded edges make them friendlier to your clothes and other items in your bag than anything with harder corners or sharper edges. They can typically be picked up at dive stores for 2 or 3 dollars.
I took this approach on a recent cruise, where we took only the base set of cards. All of the cards fit in one "box", with some room left over, if you wanted to added favorite cards from another expansion. I could have put Intrigue into a second box, but my girlfriend and I are relatively new to the game so the base set was enough to satisfy our addiction. This approach was also easier than taking two laptops and fighting intermittent internet access to play on Isotropic.
I got around the "no labels = no card organization" problem as follows. Rubberbands kept four basic subsections together: One was all the money cards, one was 12 (x10) kingdom cards, one was the other 13 (x10) kingdom cards. The last subsection was as follows, separated by the various blank cards and the Trash mat: Two starting hands, the 3 victory card piles of 8 cards each, the randomizer deck, 10 curse cards, and all the remaining "extra cards" not needed for 2 person play. Set up was relatively quick, even with having to locate the kingdom cards for the 1st game - each of us simply took the stack with (roughly) half of the kingdom cards. For subsequent games, finding the new kingdom cards was even easier. After using the randomizer deck, any cards to be retained from the previous game were pulled aside for reuse, the not-to-be-reused cards were stacked out of the way, then we each took one of the (now smaller) piles of kingdom cards to quickly find those that were needed. It worked much better than I thought it would, and may actually have been faster than constantly returning cards to labeled slots in a box.