There are many ways to organize it but I chose to do it according to the DMC Colour Chart. Here is just a piece of the chart, the rest is found here: http://orangethread.blogspot.com/2012/05/dmc-colour-chart.html

The container I bought had these little cards in, which works great for your thread. If you cannot find them, there are loads of great tutorials here on Cut Out & Keep.

I have stray pieces of embroidery thread which use to lay around, which later started to resemble bundles of knotted useless embroidery thread. Sometimes these pieces can come in handy so I decided to sort my little problem out.

I used thick cut off pieces of cardboard, cut them into strips which would fit into my embroidery container, punched a few holes in the bottom, and cut slits in the top.

The size and the number of holes really depends on your needs.

See, nice and organized.