A plethora of studies on self-organization has been carried out in broad areas including chemistry, biology, astronomy, medical science, telecommunications, etc., in both academia and industry. Following the studies on swarm intelligence observed in social species, the artificial self-organized systems are expected to exhibit some intelligent features (e.g., flexibility, robustness, decentralized control, self-evolution, etc.) that may have made social species so successful in the biosphere. In this paper, the application of swarm intelligence in communications networks will be studied, and we survey different aspects of bio-inspired mechanisms and examine various algorithms that have been proposed to improve the performance of artificial systems. Some fundamental self-organized networking (SON) mechanisms, designing principles and optimization approaches for artificial systems will then be investigated, followed by some well-known bio-inspired algorithms (e.g., cooperation, division of labor, distributed network synchronization, load balancing, etc.) as well as their applications to the maintenance/operation/optimization of artificial systems being analyzed. Besides, some new emerging technologies, such as the Self-X capabilities and cognitive machine-to-machine (M2M) optimization for the 3rd Generation Partnership Project (3GPP) Long Term Evolution (LTE)/LTE-Advanced systems, are also surveyed. Finally, the remaining challenges to be faced in designing the future heterogeneous systems will be discussed.