The blue bobbin case is not really blue, it's black like your regular one. It just has a blue dot on it. The regular bobbin case has a red dot on it. It is used for FMQ or embroidery when you need a looser tension. It has nothing to do with the blue colored bobbins or the pink ones for that matter that are collector items from Janome.
Ah, Rainbowcat beat me to it. Thanks.