WiMAX with femto-cells is a cost effective and spectrally efficient next generation broadband wireless communication systems. Femtocells are perceived as having a strong potential to provide high data-rate services with increased coverage at low cost. Femtocells will allow new services and business models to be offered to indoor users. Almost parallely, the WiMAX standard has emerged as a potential candidate technology for the future wireless networks. WiMAX femtocells are currently under development and will therefore play an important role in the world of indoor broadband wireless access. However, several aspects of this new technology, such as the access method and interference avoidance techniques play a crucial role in the amount of interference caused to co-channel deployed macrocells. Cognitive radio is a recent technology which enhances spectrum efficiency by dynamic spectrum sensing. So by the integration of WiMAX with femto-cells and cognitive radio further enhances the spectrum efficiency. The integration faces certain challenges in terms of frequency reuse, power control, interference, complexity etc. So it is required to find the optimum power that is to be transmitted from the base station and also the optimum routes with optimum channel allocation, so that the interference is reduced and frequency reuse is possible. Also by implementing multi-hop cooperative communication, complexity of the problem further increases. The constraints are mathematically modeled using stochastic network model. Three resource allocation policies are introduced and it is proved using Lyapunov theory that these policies leads to the throughput enhancement. It is showed that how relaying and co-operative relaying affect the throughput. At-last an algorithm is presented for resource allocation satisfying the objectives of the policies. © 2005 - 2012 JATIT & LLS.