Mastering networks has become one of the major challenges in modern societies where constantly new links among entities on different scales are created or discovered, ranging from molecules to the interactions of societies on a global level. This has lead to a variety of theories and their applications in different branches of science, from physics and chemistry to ecology and economics. The UniNet consortium tries to create the basis for the unification of network theories for applications in different areas, especially genetics, biochemistry, neurosciences, ecologyand economy. This proceedings volume contains the contributions to the UniNet workshop 2006 with short overviews, examples for data generation in the different fields and the state-of-the-art of the projects within UniNet.