The two most logical (to me, anyway) systems I've seen recommended for organizing yarn are
1) by size, from laceweight up through chunky, and
2) by fiber, with whatever is 50% or more being the controlling factor.
Using system 1), all of your sock-weight yarn, for example, is together, so if you decide to make socks, you don't have to go through all your yarn to find sock weight.
Using system 2), all of your wool / alpaca / cotton / whatever yarn is together, so if you decide to make a warm / cool sweater or top, you can look in the best location. Unfortunately, using this system, if you decide to make socks, the sock-weight yarn may be in different locations....each system has its advantages and disadvantages.
I've done mine by weight. I had so much worsted and bulky, though, that they had to be divided according to fiber content. Now I can lay my hands on what I'm looking for pretty quickly.