Complexity of current computer networks, including e.g., local networks, large structured networks, wireless sensor networks, datacenter backbones, requires a thorough study to perform analysis and support design. Simulation is a tool of paramount importance to encompass all the different aspects that contribute to design quality and network performance (including as well energy issues, security management overheads, dependability), due to the fact that such complexity produces several interactions at all network layers that is not easily modellable with analytic approaches. In this systematic literature review we aim to analyze, basing our investigation on available literature, the adoption of a popular network simulator, namely ns-3, and its use in the scientific community. More in detail, we are interested in understanding what are the impacted application domains in which authors prefer ns-3 to other similar tools and how extensible it is in practice according to the experience of authors. The results of our analysis, which has been conducted by especially focusing on 128 papers published between 2009 to 2019, reveals that 10% of the evaluated papers were discarded because they represented informal literature; most of the studies presented comparisons among different network simulators, beyond ns-3 and conceptual studies related to performance assessment and validation and routing protocols. Only about 30% of considered studies present extensions of ns-3 in terms of new modules and only about 10% present effective case studies demonstrating the effectiveness of employing network simulator in real application, except conceptual and modeling studies.