In resource constrained wireless systems, achieving higher spectral efficiency (SE) and energy efficiency (EE), and greater rate fairness are conflicting objectives. Here a general framework is presented to analyze the tradeoff among these three performance metrics in cooperative OFDMA systems with decode-and-forward (DF) relaying, where subcarrier pairing and allocation, relay selection, choice of transmission strategy, and power allocation are jointly considered. In our analytical framework, rate fairness is represented utilizing -fairness model and the resource allocation problem is formulated as a multiobjective optimization (MOO) problem. We then propose a cross-layer resource allocation algorithm across application and physical layers, and further devise a heuristic algorithm to tackle the computational complexity issue. The SE-EE tradeoff is characterized as a Pareto optimal set, and the efficiency and fairness tradeoff is investigated through the price of fairness (PoF). Simulations indicate that higher fairness results in a worse SE-EE tradeoff. It is also shown imposing fairness helps to reduce the outage probability. For a fixed number of relays, by increasing circuit power, the performance of SE-EE tradeoff is degraded. Interestingly, by increasing the number of relays, although the total circuit power is increased, the SE-EE tradeoff is not necessarily degraded. This is thanks to the extra degree of freedom provided in relay selection.