Only Sandy Bridge Extreme and the newer Ivy Bridge CPUs have full support for Pcie 3. Even then the performance increase over pcie 2 is marginal at most 5%.
To have full support of pcie 3, the cpu and motherboard must be compliant.
as grebgonebad mentions, graphics cards will work with either pcie version, so i wouldn't concern yourself with a slight increase from pcie3.
Give it a few more years and pcie4 will be out and graphics cards in this era will probably start utilizing pcie3 properly and the same argument here will apply about pcie4 and it's worthiness at the time
Yes. 3.0 is backwards compatible with 2.0. Think along the lines of USB2 working in USB3 ports. =)
it means i can run it 3.0 in 2.0 , but i cant get the full performance or speed of 3.0
You will be able to run a 3.0 GPU in a 2.0 socket at 2.0 speeds. In order to get the full potential of 3.0 you need to plug it into a 3.0 socket, however it is not essential as it will work in either.
Chances are that the graphics card you are planning to use won't be able to saturate PCIe 2.0 x16, so you won't take a performance hit by using your card in a PCIe 2.0 x16 slot.