I sort my yarn by weight, color and brand. All of my worsted weight yarn is sorted by similar or very contrasting color. For example I have reds and oranges in one box, but yellows and greys/black in another and so on. I have 1 tub that has all Lion's Brand Hometown USA. I got a lot of it on sale during Black Friday. Until I use it all, it will just stay in it's own tub because there is so much of it. I have a tub for all Bulky #5 yarn and another for Super Bulky #6 yarn. Also the novelty fun fur yarns get their own box. There are also tubs for the variegated yarns that have multiple colors in the skein. The colors I use the most I have put on the shelves so I can get to it easier.
I also utilize these canvas storage boxes I got at Walmart on clearance for $3. They have a metal frame inside and hold up really well!
So that's it! That's how I organize and store my yarn! Not necessarily pretty, but very functional for me!