Question: I want to connect a PCIe 16x 3.0 GPU card to a Raspberry pi. I don't mind lo loose bandwidth, i just want to use the core GPU capabilities. So, the only idea that came out to my mind is to use the 26 GPIO RPi pins. I am concern about the GPIO/PCIe programing, do not have any idea neither an approach. Is this a crazy a idea ? can somebody help me to get a big picture of what i must to do ?

Answer: 
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.
A few sites have tested the Pi's gpio speed and a quick search shows speeds on the order of hundreds of KHz. Not sure of the PCI 3 frequency off the top of my head but I believe each data line runs in the MHz range. 

The low frequency of the GPIO coupled with the coding overhead for each pin it would be impossible to bit bang the Pi fast enough.