Recent studies of complex systems indicate that real networks are far from random, instead having a highly robust, large-scale architecture that is governed by strict organizational principles. Here, we will focus on cellular networks, discussing their scale-free and hierarchical features. We will first discuss a few central network models, before illustrating the major network characteristics using examples primarily from bacterial metabolic networks. Additionally, as the interactions in real networks have unequal strengths, we discuss the interplay between network topology and reaction fluxes in cellular metabolic networks, as provided by the flux balance method. We find that the utilization of the metabolic networks is both globally and locally highly inhomogeneous, dominated by “hot-spots” that represent connected set of high-flux pathways.