GPIO/PCIe programing
The GPIO pins on the Raspberry Pi are not even close to being fast enough (maybe a couple of MHz vs several GHz required for PCI-E). You can however, check this out: http://hackaday.com/2012/10/08/stm32-driving-a-pcie-video-card/

This doesn't use the PCI-Express interface at all, but some Radeon GPUs have a 'debug bus' which can be used to write internal registers at low speeds, apparently through I2C, which the Raspberry Pi can interface to. It looks like the code got taken offline (probably NDA stuff, or the original author is trying to make a business out of it). If you had a couple of months to spare and experience with hacking Linux drivers, you can probably replicate his work by looking at the open source Linux drivers.