Various network topologies can be used for deploying High Performance Computing (HPC) clusters. The network topology, which connects switches In cabinets on a machine room floor, is typically defined once and for all at system deployment time. For a diverse application workload, there are downsides to having a single wired topology. In this work, we propose using free-space optics (FSO) in large-scale systems so that a diverse application workload can be better supported. A high-density layout of FSO terminals on top of the cabinets is determined that allows line-of-sight communication between arbitrary cabinet pairs. We first show that our proposal reduces both end-to-end network latency and total cable length when compared to a wired topology. We then demonstrate that the use of FSO links improves the embedding/partitioning capabilities of a wired topology. More specifically, we show that a recently proposed random low-latency topology can be augmented with a reasonable number of FSO links to support multiple k-ary n-cube and fat tree embedded topologies. Finally, we investigate power-aware on/off link regulation techniques and show how adding/reconfiguring FSO links leads to both performance and power efficiency improvements.