Gen3 means PCIe 3.0 support with the new Intel CPUs - Ivy Bridge. Next year, Q2 Intel will release the new line of processors and AMD/Nvidia will release Gen3 graphic cards. If you buy Gen3 board, and than next year buy new processor and graphic card you will be able to enjoy the PCIe 3.0 speed for transfer of data between the CPU and the GPU. Gen 3 boards offer native Ivy Bridge support in the bios while non gen3 will most probably require a bios update and still only PCIe 2.0 speed.
I would go with Gen3 only if I plan to use PCIe 3.0 graphic cards or use SSDs with PCIe 3.0 controllers.
All this does means nothing to users building mainstream configurations and do not plan upgrades next year. For enthusiasts it means a lot.
Oh, I am sorry for the double post. I forgot to mention that the boards are basically the same except the Gen3 switches.
I had P8P67 Deluxe teamed with I5 2500K before the current one P8Z68 V-Pro Gen3 and I love it. Great overclocker, great bios as all motherboards from ASUS in this class and no problems at all with I7 2600K @ 5.0 GHz.