I'll use logistics as an example.
Say your GPU is your shipping warehouse. It can send out 100 trucks a day to a different warehouse. Think of PCIe as lanes on a highway. On your old mobo, you had 8 highway lanes, you've now increase the highway to 16 lanes. Yet your warehouse can only send 100 trucks a day.
The way to increase your performance is to get more trucks on the road.
You'll see more performance gains by moving to a better graphics card. Substantial increase would be for Nvidia: GTS 250 or higher. Moving to 9800GT is not worth it.
Just want to add, it will take a GTX295 or HD4870X2 to fill the bandwidth of PCIe 1.0.