We study the joint allocation of three types of resources, namely, power, subcarriers and relay nodes, in cooperative two-hop multi-relay OFDM systems. Each relay adopts the amplify-and-forward (AF) protocol. The objective is to maximize the system transmission rate subject to individual power constraints on each node. We formulate such a problem as a subcarrier-pair based resource allocation that seeks the joint optimization of subcarrier pairing, subcarrier-pair-to-relay assignment, and power allocation. Using a dual decomposition method, we solve this problem efficiently in an asymptotically optimal manner. We further propose two suboptimal algorithms to trade off performance for complexity. Simulation results demonstrate that the proposed subcarrier-pair based resource allocation schemes significantly outperform the symbol based benchmark scheme. Moreover, it is shown that subcarrier pairing plays an important role in improving the system performance.