Grab some pipe cleaners. (I would have preferred white ones instead...but all I could find were the neon ones)
Grab spools of thread and matching bobbins.
Thread the pipe cleaner through the spool and bobbin, then cut the excess pipe cleaner off (leaving about 1/2" or so to fold over each end). You can get 3 spools/bobbins out of each pipe cleaner. This is also great for when you have several bobbins of the same color - just cut the pipe cleaner a little bit longer to accommodate the extra bobbins.
Here is where my thread is kept. This is one of those laundry/utility room plastic drawer units.
The top drawer is for white/black/gold shades.
Next is the blue and green drawer.
Then the red, orange, and yellow drawer.
The bottom drawer is for pinks and purples.
I used to use rubber bands, but I would never take the time to band the spool and bobbin back together once I was done sewing. I think this will be much easier to stick with!