The last decade has witnessed a rapid proliferation of superscalar cache-based microprocessors to build high-end computing (HEC) platforms, primarily because of their generality, scalability, and cost effectiveness. However, the growing gap between sustained and peak performance for full-scale scientific applications on conventional supercomputers has become a major concern in high performance computing, requiring significantly larger systems and application scalability than implied by peak performance in order to achieve desired performance. The latest generation of custom-built parallel vector systems have the potential to address this issue for numerical algorithms with sufficient regularity in their computational structure. In this work we explore applications drawn from four areas: atmospheric modeling (CAM), magnetic fusion (GTC), plasma physics (LBMHD3D), and material science (PARATEC). We compare performance of the vector-based Cray X1, Earth Simulator, and newly-released NEC SX-8 and Cray X1E, with performance of three leading commodity-based superscalar platforms utilizing the IBM Power3, Intel Itanium2, and AMD Opteron processors. Our work makes several significant contributions: the first reported vector performance results for CAM simulations utilizing a finite-volume dynamical core on a high-resolution atmospheric grid; a new data-decomposition scheme for GTC that (for the first time) enables a breakthrough of the Teraflop barrier; the introduction of a new three-dimensional Lattice Boltzmann magneto-hydrodynamic implementation used to study the onset evolution of plasma turbulence that achieves over 26Tflop/s on 4800 ES promodity-based superscalar platforms utilizing the IBM Power3, Intel Itanium2, and AMD Opteron processors, with modern parallel vector systems: the Cray X1, Earth Simulator (ES), and the NEC SX-8. Additionally, we examine performance of CAM on the recently-released Cray X1E. Our research team was the first international group to conduct a performance evaluation study at the Earth Simulator Center; remote ES access is not available. Our work builds on our previous efforts [16, 17] and makes several significant contributions: the first reported vector performance results for CAM simulations utilizing a finite-volume dynamical core on a high-resolution atmospheric grid; a new datadecomposition scheme for GTC that (for the first time) enables a breakthrough of the Teraflop barrier; the introduction of a new three-dimensional Lattice Boltzmann magneto-hydrodynamic implementation used to study the onset evolution of plasma turbulence that achieves over 26Tflop/s on 4800 ES processors; and the largest PARATEC cell size atomistic simulation to date. Overall, results show that the vector architectures attain unprecedented aggregate performance across our application suite, demonstrating the tremendous potential of modern parallel vector systems.