I don't separate by expansion. I separate by type (terrain, trap, event, etc...) and store them in numerical order, keeping crawler and dungeon cards separate, of course. This makes it much easier for me to build decks quickly.
Oh yeah, separating by types is a good idea indeed. Since the campaigns do not include the cards' numbers, I will probably order them by names.
Do you also merge the Thorn and the Mines with the rest of the cards?