Thus far I've only had occasion to use DMC floss. I keep them in numerical order on plastic bobbins in the DMC floss boxes... and even the DMC stickers. I'm a sucker, what can I say.
(Somewhat ridiculously, one of those floss boxes, complete with 50 plastic bobbins, sells at my local Michael's for $2.99... and a package of 28 plastic bobbins by themselves sells for $3.50.
On a project, I keep the bobbins together in a Ziploc bag. I used to cut off single strands, but now I cut off a whole length at once and store the remaining strands by tying them onto the hole with a ring knot. As I generally like to finish entire colours at once if the project lends itself to that, I return used colours to the box as I go.
And I keep track of my floss using the Cross Stitch Guild's iPhone app
I haven't yet done one of the ginormous projects with zillions of colours; if I do it'll take some thinking to come up with a more efficient system for floss management during projects...