As we integrate hundreds of cores in the future, energy-efficiency and scalability of Network-on-Chips (NoCs) has become a critical challenge. In order to achieve higher performance-per-Watt than traditional metallic interconnects, researchers are exploring alternate energy-effident emerging technology solutions. In this paper, we propose to combine two emerging technologies, namely 3D stacking and nanophotonics that can deliver high on-chip bandwidth and low energy/bit to achieve a high-throughput, reconfigurable and scalable NoC for many-core systems. Our simulation results indicate that the execution time can be reduced up to 25% and energy consumption reduced by 23% for Splash-2, PARSEC, SPEC CPU2006 and synthetic benchmarks for 64-core and 256-core versions.