So i am wanting to use the gtx 680 on a new system that i am build but will using a 2.0 mother board on a 3.0 video card will this bottleneck its performance and also wanting to know if what i have will work with the gtx 680 and not bottleneck it?
ASUS Sabertooth 990FX AM3+ AMD 990FX SATA 6Gb/s
AMD FX-4100 Zambezi 3.6GHz (3.8GHz Turbo) Socket AM3+
G.SKILL Ripjaws Series 16GB (4 x 4GB) 240-Pin DDR3 SDRAM DDR3
COUGAR COUGAR-GX1050 1050W ATX12V / EPS12V SLI Ready CrossFire Ready 80 PLUS GOLD
cooler master haf 922
Your processor will perform noticeably less than your graphics card if you decide to go with the GTX 680, I would suggest going with an Intel CPU unless you are already committed to the AMD CPU or at least go with the FX-4170. You could also go with a GTX 580 which would be more on par with your CPU and bypass the whole PCIe 2.0/3.0 issue, although the performance difference between 2.0 and 3.0 is only evident in extreme systems in games with extreme demands, not the majority of games. Going this route would also allow you to save some money in other areas of your build, the 16GB of RAM can be scaled down to 8GB (2x4GB) and getting a lesser power supply (500-600W). You could use this extra money to justify the jump in processor and maybe get a Solid State Drive that would make your system much more responsive and decrease load times.
Hope that makes sense to you. See this for Graphics Cards and this for CPUs.