I use DMC Embroidery Floss the most so I keep it in order and easy to access. My grandfather made these wood storage boxes for me many years ago. The floss is filed by numbers in groups:
150-225
300s
400s
500s
600s
700-747
754-
800s
900-948
950-
3000s-3700s
3800s
Each color is kept in a baggie labeled with its number. I keep a basket next to the boxes to hold skeins that need to be filed.