When I'm following a pattern it's obviously best to have the thread stored by number so I can easily see whether I have what I need. But if i want to be more experimental, use my own design or alter a design then it's helpful to have all the shades of the same colour together.
For now I've gone for the logical answer of storing them by number it works for most of them but my third (yes I need three boxes to store them!) box has all the higher numbers in and non-anchor threads so it's a bit of random selection and look at pretty!
There's also my forth box - which I use to stored the threads for my current project.
I love my threads!