The continued reduction of semiconductor device feature sizes towards the single-digit nanometer regime involves a variety of quantum effects. Modeling quantum effects in phase space in terms of the Wigner transport equation has evolved to be a very effective approach to describe such scaled down complex systems, accounting from full quantum processes to dissipation dominated transport regimes including transients. Here, we discuss the challanges, myths, and opportunities that arise in the study of these complex systems, and particularly the advantages of using phase space notions. The development of particle-based techniques for solving the transport equation and obtaining the Wigner function has led to efficient simulation approaches that couple well to the corresponding classical dynamics. One particular advantage is the ability to clearly illuminate the entanglement that can arise in the quantum system, thus allowing the direct observation of many quantum phenomena.