Not any time even remotely soon IMHO.
There is still an extremely large market for PCI graphics cards for motherboards with integrated video without an AGP expansion port.
Precious few servers even have an AGP expansion port, and a large number of those don't have integrated graphics... those that do often install a seperate PCI graphics card for multi-monitor.
I don't see PCI graphics cards going anywhere for the next 5 years at a minimum, and I think it highly likely we will continue to see "high performance" PCI graphics cards for the next 2 years at a minimum.
PCI graphics cards have a large market in the Pro 2D graphics design wherein 5-6monitors connected to a single system arent terribly unusual, in such a scenario there are few AGP boards around that can drive 4+ monitors so it's common practice to use PCI to expand that.
We are certain to see PCI-X based graphcis cards, but even PCI 2.2/2.3 compliant graphics cards should have a long life-span ahead of them.