An ad hoc network comprises mobile devices with limited computing and energy resources together with wireless communication, which have to cooperate to provide networking services. This communication scenario presents many specific challenges that make ad hoc networks very different from traditional wired and wireless data networks. It makes classical approaches for network analysis insufficient. To deal with the design, implementation and test of this innovative communication paradigm, simulation techniques are of primary importance, since they allow to specify the level of detail of the simulated model. At the same time, the complex interaction among different entities make the performance evaluation of real ad hoc systems through simulation very hard. This chapter discusses traditional simulation strategies for ad hoc networks, highlighting their limits, drawbacks and possible overcoming. It presents efforts of the research community in improving the quality of simulation analysis according to different aspects, such as metrics definition, model design and simulation tools extensions. Then, the chapter focuses its attention on the benefits that the Discrete Fourier Transform analysis can produce if it is applied on simulation data. It describes a detailed methodology to gather and elaborate simulation measurements in order to avoid loss of information on rare events that occur in simulations. The presented methodology gets advantages (such as simplicity and flexibility) from simulative investigation approaches and, at the same time, offers a new analysis tool suitable for both protocol debugging and system performances evaluation. In fact, it transfers time-dependent measurements into the frequency domain, allowing to point out the occurrence of events which take place only under particular conditions and to detect occasional misbehaviors of the system.