You should be ok saving money and getting the 560. From what I understand you can choose to use the lucid virtu chip on the mobos to have the cpu's gpu do encoding and stuff....but I've read you can also use the cpu's gpu just like another installed graphics card and run another monitor off it.
The only reason you would need pci-e 3.0 is if you're going with high end sli or crossfire. I wouldn't worry too much about it otherwise. The only difference between 2.0 and 3.0 is going from 5GT/s to 8GT/s. They claim it doubles the bandwidth because of optimizations, but you still don't saturate 2.0 with a single card. I think 5GT/s is something like 8GB/s across the 16 lanes. As an anecdotal example, I've read that 8800gt cards only used about half of the 4GB/s in pci-e 1.0. So if you're planning on buying super high end cards, or running crossfire I would shop around for a pci-e 3.0 board.
There's a test of this on hardocp, where they ran gtx480s in sli. They tried them at 16x/16x, 16x/8x, 8x/8x...at different resolutions. Their conclusion was that 8x/8x had a performance impact @ 5760x1200, but 16/8 only had a minuscule effect on performance even at 5760x1200 resolution.
The short answer for mobos is that theoretically, if intel's spec is followed, it doesn't make a big difference how many power phases you have. But, if you're overclocking you'll probably have more success with a decent number of power phases. It will probably make for a more stable voltage to the cpu etc under higher heat conditions, and if you need to supply more voltage to the components.
edit: Also, for what mobo you should get. I got that one because I got $80 off it during a sale, but it was also on my short list anyway. If you want to wait a week, I should have my parts by Thursday, so I can let you know if there are any issues with the board.
Edited by Bard, 18 October 2011 - 07:39 PM.
Rule #76: No excuses. Play like a Champion!