Marceline's Confectionery is owned by Disney, so they do accept Disney gift cards. So do/should WOD, the Disney Home Store, WonderGround Gallery, the Disney Dress Shop, the Dream Boutique, and Pin Traders. As stated above, the non-Disney owned restaurants and businesses in DTD do not accept Disney gift cards.
ETA: Just to update: It appears that the Dream Boutique might be gone (as of 3/24) -- the store windows are papered over with signs for the Disney Dress Shop -- so it seems the Dress Shop will be moving soon to that spot so that the restaurants can move in to their old spot.