This benchmarking is only of the proprietary NVIDIA Linux graphics drivers on each platform. Linux users also have the option of running the open-source "Nouveau" graphics driver that's developed by the open-source community through reverse-engineering the NVIDIA binary graphics driver. However, its performance isn't up to scratch nor are other features like the level of OpenGL compliance, power management, and vendor-specific items like SLI / PureVideo VDPAU, etc. Of the three graphics cards being tested, the GeForce GT 220 has worked at times with Nouveau but currently as found in Ubuntu 12.10 is in a regressed state: the driver goes awry during mode-setting. The GeForce GTX 460 "Fermi" and GTX 680 "Kepler" graphics cards also have no re-clocking support within the Nouveau driver right now so their clock speeds are stuck lower, plus with the latest-generation GeForce 600 series, there isn't even support in a released mainline kernel for initializing the hardware with acceleration support unless dealing with the FUC microcode situation.
Benchmarking on Windows and Linux was handled in a fully automated and reproducible manner using the open-source Phoronix Test Suite software and OpenBenchmarking.org infrastructure. The OpenGL benchmarks used were ones that offer native versions for both Windows and Linux that are of similar quality.