For desk top or pipe shelf, a pencil/pen holder might do the trick, especially if you keep a good supply of pipe cleaners on hand. Or you could put a piece of folded cardboard in there if your supply dwindles and you want to keep them upright. The high price cigar tube sounds like a winner for a portable pipe cleaner case, and
it gives you an excuse to buy and smoke a fancy cigar. Dill's cardboard case is also excellent. The inside pocket of a sports jacket or suit jacket will keep pipe cleaners
in pretty good shape if you don't use it otherwise, but don't put pipe cleaners in any garment you would run through the washer or dryer; you don't want those little wires in the laundry machine gears.