I've been using these Hand-i-bobs for years.
http://www.amazon.com/Handi-Bobs-HB1...ywords=bobbini (Keep looking until you find a good price. These press into the spool's hole and keep matching bobbins firmly attached to avoid confusion. They will fit almost every thread type I have (except Superior Masterpiece spools). For those I've been using little pink plastic pegs that I can no longer find. For those I expect this item on Amazon would do the trick
http://www.amazon.com/Bobbin-Buddies...bobbin+keepers Or or a pipe cleaner.