What is a good way to store multiple expansions of Dominion?
I got a 3,000 card box from the local gaming store and then printed off a cardstock set of tab dividers from Board Game Geek (I use the Sumpfork tabs). All cards go alphabetically instead of by set, except for the cards common to all games. Prizes are stored with Tournament, because that's the only scenario in which you would need them.

To simplify setup of Victory/Curse cards, I change the direction of the cards. For Victory cards, the first 8 face forward and the second 4 face backwards so I can easily separate out the cards not needed for a 2 player game. I do the same with Curses: 10 forward, next 10 backwards, final 10 forwards. Estates get complicated; I do 8 forward, 4 back, then 4 sets of 3 alternating forward and back (for starting hands). I could do alternating sets of 7 Coppers as well, but I haven't gotten around to it.