I've seen a lot of different systems on here for storing cross stitch thread. I thought I would share mine with everyone.
I use ziplock snack size storage bags, index cards and plastic shoe boxes. I print the number and name on a sticker that I place on each index card. The index card goes into the storage bag, which helps to hold it upright. I can see all my floss very easily. Finding the number I need is easy when thumbing through. So far I only have one shoe box of thread. Before I took a break from stitching I had three plastic boxes of thread on bobbins. After retrieving it from storage I found that it had a moldy smell to it, so I'm starting my thread collect from scratch.
When I pull my thread for a project I'll put those specific storage bags in a separate shoe box. If I'm using the same color in two projects I'll make up a separate index card and storage bag for the second project. When I complete I put the extra index cards in one storage bag. They'll be there to use if ever needed again.
I also punch a hale in the top corner of each bag to allow for some air flow.