they will be backwards compatible. gen 3 is not useful on even the 7970 right now. The only thing gen3 does now is that it lets you use the x4 pcei slot without loss of performance.. For Pcei gen 2...x8 is more than enough.
PCI-E is the slot or interface that your graphics card goes to. It connects to the processor/CPU through a hyper-transport. x4 and x8 is the bandwidth of the slots, so x16 will be faster than x8, x8 will be faster than x4 and continues...
Anywhere you put the GPU, on x16/x8/x4, it would be fine, but will be slower when you put it on lower bandwidth.
Usually entry level (Sub $100) will be fine with x4 with minor bottlenecks
Mid range and high end cards (From $100 Up to $500) usually be fine with x8, just cards like 7970 or GTX 580 face bit of bottlenecks I think.
Extreme Cards (Above of $700), to be save without bottlenecks, need x16.
Basically all you need is x8, except you buy extreme cards like HD 6990 or GTX 590.
EDIT: Forget on the track of the thread...
All you actually need is PCI-E 2.0, but if you can get a same motherboard with a PCI-E 3.0 support in it, go with that. It's usually a $10 maximum difference. But when you have to buy a Sandy Bridge-E and a X79 Motherboard for example, there is no point of that. Go get a P67 and i5-2500k if this was the case.
But as I said if you can find a good PCI-E 3.0 Motherboard which the price is not far (Max $10) from a PCI-E 2.0 one, it's good to have it.