Quantum aggregates are assemblies of monomers (molecules, atoms, quantum dots...), where the monomers largely keep their individuality. However, interactions between the monomers can lead to collective phenomena, like superradiance or efficient excitation transfer. We study different kinds of aggregates (e.g. light harvesting systems, arrays of Rydberg atoms, self-assembled organic dyes...) Using various methods (ranging from Green-operator methods over stochastic Schroedinger equations to semicalssical surface hopping) we study optical and excitation transport in these systems. Of particular interest is the coupling of the excitation to nuclear degrees of freedom.