This paper addresses the allocation of link capacities in the automated design process of a network-on-chip based system. Communication resource costs are minimized under Quality-of-Service timing constraints. First, we introduce a novel analytical delay model for virtual channeled wormhole networks with non-uniform link capacities that eliminates costly simulations at the inner-loop of the optimization process. Second, we present an efficient capacity allocation algorithm that assigns link capacities such that packet delays requirements for each flow are satisfied. We demonstrate the benefit of capacity allocation for a typical system on chip, where the traffic is heterogeneous and delay requirements may largely vary, in comparison with the standard approach which assumes uniform-capacity links.1