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: 
If you want to hit the problem the hard way, you can bit bang the protocol with some external help.

There are several signals you need to mind: signals shared by all cards `SM_SCL`, `SM_SDA`, `PCIE_IRQ` and `PCIE_CLK`, as well as per-channel `PCIE_Rx` and `PCIE_Tx`.

Most PCI-E lines are differential signaling which should be derived externally to and from single-ended signal from your Pi. This includes all `PCIE_*` lines except IRQ. `SM_*` are SMBus which can go directly to the I2C of the Pi, and all other signals will need to be bit banged (despite with limited external hardware support).

You do not need to implement a full x16 bus, a x4 bus (uses 10 GPIOs and I2C) will be enough, if your GPU can work at that painfully slow speed.
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.