I use a lowepro case similar to the one Charade described, I do use the plastic cases that my cards came in as an extra dust barrier...
I don't mark my cards in any way, I can tell by the card that I took out of my camera, which card is next, and therefore which cards are used or empty...I always use them in a certain order,
2 gig card first, 1gig 80x speed, then 1 gig 40 x speed, for casual, leisurely shooting I will use my 4 gig microdrive.