In this paper we consider a software tool for the simulation and analysis of discrete, continuous and hybrid Petri nets, called HYPENS. It is an open source tool we have recently developed in Matlab. The main contribution of this paper is that of demonstrating the efficiency of HYPENS via real several non trivial examples. In particular, we consider a family of purely discrete event systems modeling a queueing network, and a job shop system with finite capacity buffers and unreliable multi-class machines. A detailed analysis of the computational times and of the accuracy of the results is proposed. In particular, in the first case example, that is modeled using discrete Petri nets, the correctness of the results is proved using well known analytical results from the queueing theory.