personally I wouldn't worry too much about it. you'll either drive yourself insane or spend $$$$$$$$ rebuilding/upgrading your computer every 6 months to keep up with the lastest and greatest.

all of todays cards will run all the games just fine on PCIe 1.x the only real NEED for 2.0 is video editing or just plain ego and benchmarks.

yes you will some potentail and not be able to harness the full power of the card but the only way your going to fix that is to upgrade the motherboard. the question you have to answer is are you willing to pony up $100-$300 for a new mobo just so you can avoid losing a few FPS?

then next year you'll be in the same boat again. PCIe 3.0 is in the works and at this point is expected to hit the market next yr. personally I build a new system about every 2 yrs, I build the best I can for what I can afford, I don't worry about what has become the next best thing cuz 2 versions down the road will co into my next rig.