Now, I'm not sure if this problem is something everyone already knows about or what, but in the middle of tweaking my system for DOOM 3, I did something I hadn't for quite a while: put an NVIDIA graphics card in it. (Yes, folks, the Radeon 9800 Pro 256MB card in there was running a little slower than I wanted, so I thought I'd go for the latest. I put in GeForce 6800 Ultra OC.) I was shocked to see performance drop massively with the move to the NVIDIA card. The thing would run OK in some places, but in others, it was literally a slideshow and wholly unplayable. After lots of checking settings, updating chipset drivers, and futzing about, I figured out that the problem was this: I have two monitors on my system. Turning off the output for second monitor (by unchecking "Extend my Windows desktop onto this monitor) immediately fixed the problem. Maybe there's a more elegant fix—I would like to think so—but that worked for me. If you own an NVIDIA card, you may need to try this.
News source: The Tech Report