PCI-Express 16x is the newest generation of slot types, and has a higher lane speed than the previous-gen AGP 8x. In a sense, PCI-E can be 2x faster than AGP 8x. However, most computer users still use AGP, so card companies still make AGP versions of new video cards that arrive. For gaming, you need to get PCI-E slots for upgrading future cards, because AGP may disappear some day.
As far as Intel Dual Cores, if you really want to go with them, I recommend the Pentium D 830 3.0Ghz 800Mhz FSB Smithfield EM64T processor.