Taking full advantage of PCI Express 2.0 for Radeon graphics cards involves setting a few registers related to the PCI-E link width and speed control. The code has been there for the supported generations of Radeon hardware for many months now, but it is not on by default.
Like the Intel RC6 and Active State Power Management problems in the Linux kernel, PCI-E Gen2 is not on by default at this time due to a few hardware-specific problems. For some problematic systems, having the Radeon DRM with PCI Express 2.0 support enabled will cause a corrupted screen upon mode-setting. The problem comes down to compatibility issues with some motherboards. For over a year now the PCI-E Gen2 support has been concealed behind a kernel module parameter.
Those wishing to take advantage of PCI Express 2.0 with supported motherboards (nearly all Intel and AMD motherboards from 2008 and newer) and graphics cards (Radeon HD 3000 series and newer) must boot the kernel with the "radeon.pcie_gen2=1" on the kernel command line (or probe the radeon DRM with "pcie_gen2=1"), otherwise the graphics card will still be operating at PCI Express 1.0 speeds. Even with the forthcoming Linux 3.3 kernel, PCI-E 2.0 support is still off by default with the Radeon driver.