This paper addresses cooperative control problems in heterogeneous groups of linear dynamical agents that are coupled by diffusive links. We study networks with parameter uncertainties, resulting in heterogeneous agent dynamics, and we analyze the robustness of their output synchronization. The networks under consideration consist of non-identical double-integrators and harmonic oscillators. The geometric approach to linear control theory reveals structural requirements for non-trivial output synchronization in such networks. Furthermore, a clock synchronization problem and a circular motion coordination problem are discussed as applications corresponding to these two network types. The results are illustrated by numerical simulations.