With recent and rapid advances in areas such as online games, embedded systems and Internet of Things,the traditional notion of what constitutes a system is fundamentally changing.Similarly to Systems of Systems (SoS) these systems are heterogeneous, autonomous and allow dynamic and emergent configurations that evolve and adjust over time. Also, these systems allow automated optimization of system performance.Regarded as the new digital business paradigm, these types of systems offer fundamentally new ways for software development companies in their service-and value creation. At the same time, they present challenges in these organizations. In this paper, and based on multiple case study research in three different domains, we identify emergent system characteristics that pose new challenges on software development and we outline the transition towards new ways-of-working in software development.