I'd pick the Q9650, assuming you can get the Q9650 and the QX6700 for the same price. A Q9650 can easily get to 4Ghz, and it's faster and cooler than the QX6700 at the same clocks.
I'd lose any nvidia boards (they do make horrid chipsets and just got worse with the 780i/790i, you can find more about all the issues with a simple google search). Also lose the GTX 280 and get an X38 DDR2 board with an HD 4870 X2, you will get A LOT better performance for your money.
what resolution is your monitor that you are gaming on? that will impact your decision.
4870x2 is going to beat gtx280 and even beats 2x gtx280 in a lot of stuff. depending on your resolution i would recommend p45 board and a 4870x2 or x38 board (which would allow you to add another one down the road). adding another one will depend on your resolution and how soon. if too far down the road might as well just get the next good card.
get the wd 640gb hdd over the seagate 400gb. at $85 best price per gig you are going to find and is fast as well.
+1 to q9650 over the qx6700. with all of that cooling you are getting are you doing some fat over clock? if trying to go big might want 1066 ram. 800 is usually sufficient but thought i'd mention based on $$ spent elsewhere and cooling selections.
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