I use small zip lock bags from the $1 store and put one in each baggie and the treads that I cut off right straight back in as I stitch. I have a main storage plastic container with dividers that I store them in numerically and then when I work on a project I have a project plastic container that I pull out each required floss and keep it in there until the project is done then I re-file the floss back, so I inventory what I have before going to buy new floss when I start a project
I keep my floss in little baggies, and have recently put them into containers and separated them with cardboard tabs they are in numerical order and I hope one day to have the entire DMC collection :)
I used the bobbin method a few years back, but found out I dislike the folds in the floss. Now I use small Ziploc bags and sort them in numerical order.
I also have mine on bobbins and in a plastic organizer. Ive written the numbers on the bobbins though there are also stickers you can buy to put on them - Ive read they tend to fall off so Ill stick with Sharpie. My grandmother made a suggestion to me the other day which Ive started doing since Im about to have multiple projects going on. I have a gallon ziploc bag that I have my chart, floss for that project and project itself in so everything is right there together. Of course you cant very well put larger pieces in the bag, but it works well for what Im working on right now and I have it in a wooden crate next to the couch where I stitch.