Today's (15 Jan 2013) Superior Threads Newsletter included a tip on using milkshake straws --soda straws are too thin-- to keep your spools and bobbins together.
But I do organize the threads that go with current projects. Somewhere I obtained little re-sealable bags less than three inches wide and five inches deep. Into each goes a wound White bobbin, a wound Necchi bobbin, a threaded needle or a needle woven into a snippet of wool, and two spools of thread. Two spools partly because I sometimes set up both machines at the same time, and partly because the thread comes on rather small spools and I tend to run out at awkward moments.
A snack bag --an abbreviated sandwich bag-- is the perfect size and shape to contain my collection of hem gauges, but I doubt that enough people inherited a box of bias-tape cards to make hem gauges out of for that to be a generally-useful suggestion. But the bag does contain other small, flat tools that I used to have to hunt around in the drawer for.
And just today I discovered plastic bags to organize my pockets: It being cold, I took a jersey with a leak in the back-right pocket off the mending pile to wear over my regular jersey. Concerned that my keys would poke through the hole and tear it bigger, I put my key ring into a Baggie. All of a sudden, it's a *lot* easier to find my lip salve!
Perhaps I should make a little key-ring case. I had quite a lot of black ripstop left after I made my new emergency-tool case.