Motherboards do have an impact, but it is not generally significant. The best thing a motherboard can do for a video card is in the realm of higher overclocking. Brent and I have different motherboards for our testing rigs, and as such, we get slightly different figures when overclocking. Of course, the most important aspect of overclocking a video card is the video card itself. Some cards just won't do it, and some love it.
You can see the difference in the motherboards in the game benches in motherboard reviews. When the same processor is used, the difference is rarely more than 3% unless there is something wrong.
NVIDIA motherboards are supposed to give NVIDIA video cards a boost in performance with features like GPUEX and Linkboost (which was officially deleted as a feature from the 680i SLI chipset by NVIDIA recently.) These optimizations are for their video cards and just because they exist that doesn't mean that those boards sabotage the performance of ATI video cards.
Any PCIe 1.0a compliant motherboard will basically work about the same for all video cards within an acceptable margin for error. Now due to ATI and NVIDIA driver lockouts you can't compare apples to apples in an SLI/Crossfire test on the same board so your platforms have to differ. On the same motherboard regardless of chipset, the results should be about the same. In case anyone hasn't noticed yet, the so called NVIDIA chipset optimizations for their video cards are basically marketting hype and pretty much worthless.