I love using perle cotton! I buy it in Progresso, Mexico and it's inexpensive and they have beautiful colors. But alas, ziplock bags with tangled ends of thread? No fun!
I took those plastic boxes with dividers and put a ball of perle cotton in each one. I first drilled a small hole in the bottom of each divider and a little slit (like on thread spools to hold the thread taut). I have a box for each color family (sort of) and can easily see what color I want. It's working great. (pat on my own back!) I may not be the first to think of this, but I hadn't seen it before. It's kind of like the pop bottles or jars with the hole for yarn.