In order to have a good soldering joint, one must form inter-metallic layers between the solder material and the base metal. Otherwise, the solder simply solidifies over the base metal without forming any bond.
Within each inter-metallic layer, there are actually a number of different compounds formed by the solder materials and the base metal. These compounds are typically quite brittle and will adversely affect the integrity of the solder joint. As the joint is subject to stress, thermal cycles, vibration, or shock, the inter-metallic layers are usually where it starts to fail.
Since the inter-metallic layers are inevitable, it is best to keep it as thin as possible. See the guidelines for tips on minimizing the thickness of the inter-metalic layers.