Roadrunner, sit down for a moment and try to think ok? Lets assume that everything is alright with 3Dmark. If he is getting the performance he can get from his rig, why do games play worse then his 6800? Its NOT because he's running on 8x instead of 16x. Even if that had any performance impact, the 9600GT should be running as fast as (I'd argue a bit faster then) his old 6800. There is no way a 6800ultra would even max out PCIe8x. The 6800Ultra is as fast as a 7600GT, and that was on the AGP bus. The PCIe 8x is holding him back some, but its not the answer.
I thought his system was fine, but I'm wondering about his slight low SM2 score, and his low SM3. I've been looking at the ORB, and both SM2 and SM3 should be over 3000. SM2 barely is, while SM3 is not. I still think his system is more or less where it should be, I just can't figure out why the games are slower.
To the op, have you looked for patches yet? Tried any different drivers? Made sure your system is clean? (both virus and dust) LOL, did you make sure your 9600GT is plugged in?