I sort by color and if there is a small amount of one color, I combine it with another (i.e., yellow and orange) I keep in clear plastic bins -- I also put an index card on the end so I can list and read anything in the box ("batiks', large for backing', etc.) We built shelves in the baement that are the depth of a box. Two shelves keep it all -- I also have one for odds and ends, samples, freezer paper, fusibles, small pieces of batting, interfacing, etc -- all listed on a card.
I have a small rolling cart from an office supply with drawers lableled, 'needles and pins', 'thread', 'patterns', scissors, etc (includes tweezers and anything that cuts)