I had purchased the little plastic flat DMC "spools" but had not used them yet. Last night I took a few hours to undo all my skeins and wrap them onto the spools. I had just the right amount! I saved the part of each label that had the number on it and tucked that down under the thread.
I looked around the web and found a few good ideas: a Spool Rack, and also a tip for holding floss while winding it. The article I read suggested using a mason jar, but my tea was handy and the handle keep it from slipping down.
By the time I found the spool rack idea I had already wound my flat plastic spools and for now I am happy. It all fits in my plastic DMC box (which is now full).
This is only for my 6 strand floss. For my #5 Perle, I have undone and cut the skeins and looped them onto a large embroidery hoop. I can just pull on a piece from the knot and it comes right out, just one strand.
The #8 and #12 Perle cotton comes in neat balls so I have not done anything with those except put them in a box propped up against the wall. On the side is my (for now) small collection of silk ribbon. I have more on the way, so I will have to figure out something to organize that.