Wire links are used to connect to snap parts which are not readily accessible via the blue fixed length links or when the project requires parts to be mounted remotely, for example as part of a bigger STEM model.
The different colour wires are constructed identically, its only the colour of the material that is different. The normal convention used is that black links are used to connect the negative (-) side of a circuit. The crocodile clip can either be connected to a snap or to components which do not have snaps. Crocodile clips can also be connected "clip to clip" to extend the length of their reach.