© 2016 The Author(s). As steady research in wireless ad hoc and sensor networks is going on, performance evaluation through relevant network simulator becomes indispensable procedure to demonstrate superiority to comparative schemes and suitability in most literatures. Thus, it is very important to establish credibility of simulation results by investigating merits and limitations of each simulator prior to selection. Based on this motivation, in this article, we present a comprehensive survey on current network simulators for new emerging research area, three-dimensional wireless ad hoc and sensor networks which is represented by airborne ad hoc networks and underwater sensor networks by reviewing major existing simulators as well as presenting their main features in several aspects. In addition, we address the outstanding mobility models which are main components in simulation study for self-organizing ad hoc networks. Finally, open research issues and research challenges are discussed and presented.