Technically, the USB Promoter Group only suggested that plug ends and the plastic blades in the connectors be that color blue to distinguish them from USB 2.0 which is black (USB 1.1 is white). But it seems like everybody has adopted that color for internal cables too--perhaps so anyone shopping online can see the picture and know right away it has the 5 extra wires for USB 3.0.
I have seen some shady sellers hawking blue colored external cables that are only USB 2.0, now that blue has come to suggest a premium or faster product. I don't think it's any standard but yellow to red has come to represent charge-only ports like this orange one:
If you think about it, the internal cable for that could just be a 4-pin Molex