Definitely get a GTX 680 over another 295... 295's pretty outdated all around these days. PCI-E 2.0 vs. 3.0 doesn't really matter much. I'm running 2x GTX 680's on a PCI-E 2.0 board.
I don't know what socket boards the QX6700's are in, but if you could upgrade it may not be a bad idea. If you'd have to get a whole new board and CPU, it may not be worth it depending on how much extra cash you have. I remember somewhere there was a test done in Battlefield 3 with a ton of different quad core CPUs and for the most part, the CPU didn't really impact performance much as long as it was a quad core. Other games may see more improvement from a better CPU though.
Last edited by Raptor156; 05-05-2012 at 12:06 AM.
With a 680 it would not hurt to go with a nice ivy bridge, no need to break the bank either.