The fastest supercomputers today such as Blue Gene/L and XT3 are connected by a 3-dimensional torus/mesh interconnect. Applications running on these machines can benefit from topology-awareness while mapping tasks to processors at runtime. By co-locating communicating tasks on nearby processors, the distance traveled by messages and hence the communication traffic can be minimized, thereby reducing communication latency and contention on the network. This paper describes preliminary work utilizing this technique and performance improvements resulting from it in the context of a n-dimensional k-point stencil program. It shows that for a fine-grained application with a high communication to computation ratio, topology-aware mapping has a significant impact on performance. Automated topology-aware mapping by the runtime using similar ideas can relieve the application writer from this burden and result in better performance. Preliminary work towards achieving this for a molecular dynamics application, NAMD, is also presented. Results on up to 32,768 processors of IBM's Blue Gene/L and 2,048 processors of Cray's XT3 support the ideas discussed in the paper.