I don't understand why you would be getting such bad results from your PC when your 3dMark score is very close to mine, your Physics and Combined scores are actually higher than mine, this is what I got the last time I ran the test:
3DMark Score P7734
Graphics Score 10210
Physics Score 4662
Combined Score 4227
GraphicsTest 148.49 FPS
GraphicsTest 252.57 FPS
GraphicsTest 359.19 FPS
GraphicsTest 429.8 FPS
PhysicsTest 14.8 FPS
CombinedTest 19.66 FPS
I run Advanced System Care 5 to clean out the virtual cobwebs and dust bunnies from my registry and windows files, which helps, maybe you could try that and see if things improve. Alternatively have you tried putting everything back to stock speed and running the games again in case there are recoverable errors or issues being created by the overclocks? I'm not really sure what those issues might be, just clutching at straws at the moment.
Looking at the bench comparison with a 965BE the Q9550 looks like it should be able to perform fine with current games, it doesn't seem anywhere near as outdated as I thought it would be.