I found another interesting tidbit of information as I was searching for an answer to this. One forum post found mentioned turning off Aero interface option in Vista.
That has made a significant impact already. I lost the pretty transparency effects of the UI, but gained about 15 fps in windowed mode, my CPU utilization also seemed to drop, so both the CPU and GPU are hit by Aero UI.
I'm still thinking I want a newer video card, it has been 2+ years since I got the 8800 GTS.