Complex software systems are among most sophisticated human-made systems, yet only little is known about the actual structure of 'good' software. We here study different software systems developed in Java from the perspective of network science. The study reveals that network theory can provide a prominent set of techniques for the exploratory analysis of large complex software system. We further identify several applications in software engineering, and propose different network-based quality indicators that address software design, efficiency, reusability, vulnerability, controllability and other. We also highlight various interesting findings, e.g., software systems are highly vulnerable to processes like bug propagation, however, they are not easily controllable.