This thesis is devoted to the study of transportation systems by means of Complex Systems and Complex Network Theories. Complex Networks are a tools of inestimable value in human transportation studies since in most of the cases the means of transportation used by individuals to move in space are bounded to move on a complex network. The topological properties of transportation networks can influence both the ability of individuals to move as well as their behavior in the environment, thus a characterization of the network is mandatory in order to understand the properties of the considered system.The two transportation systems that have been studied in this work are the Air Transport System and the mobility of cars in a urban environment.The analysis and modeling of the Air Transport System is the first and most extensive part of this thesis. In particular we will try to characterize and study the networks in which aircraft fly, exploiting these results to build a data-driven model of Air Traffic Control.The second part of the thesis is a continuation of the studies performed during by Pierpaolo Mastroianni during his Master Thesis. His work concerned the analysis of GPS tracks data in the City of Rome and the inference of statistical laws characterizing the behavior of car drivers. My contribution to his work is the development of a model capable of explaining some of the results presented in the Master Thesis.