Yes and No. A 16x PCI Express connection is at least 190% Faster than AGP 8x but this is the connection between the system and the video card. You use the connection the most when your video card is low on memory or when the game you are using uses a Direct X or Open GL feature that isn't supported in hardware.
The short of this is: if two cards of the same chipset are available in AGP and PCI-E then the PCI-E one will always be faster. On PCI-E you don't have the overhead of the bridge chip so it's faster, and you have the better bandwidth so in intense situations such as high resolution gaming you'll come out on top every time.

related:

Cisco 10G copper cable

PCIe network card

http://my.opera.com/10gmodule/blog/2013/05/27/relation-to-multiple-access