With the current generation of GPU's, there will be little to no difference.
Newer cards may show a larger impact when they need to transfer larger amounts of data across the bus.
For some quick benchmarks on the matter, check out Tom's PCIe 2.0 test
As PCIe 2.0 has double the bandwidth of PCIe 1.1, keep an eye on the 8x PCIe results.
When compared to the 16x results, it will show how much performance you will loose going from PCIe 2.0 to PCIe 1.1.