Scraps absolutely do reproduce - just like dirty laundry!
I found a book this fall called
Cut the Scraps by Joan Ford. She recommends cutting any scraps into 5", 3 1/2" and 2" squares. Then I sort according to size and color (dark, light, etc.) in plastic containers. I don't have my sewing area totally clear but its much better! I will have to look into the Bonnie Hunter info listed above.