754 is an old socket, very bad with memory
939 is the new socket
and supports Dual Channel memoery and PCI-E
DDR2 is a new type of DDR used in INTEL ONLY systems. However due to AMD's superior memory controller, DDR in an AMD system will be just as fast / if not faster than an Intel with DDR2 at 533 mhz.
PCI-E is a good idea, and it's cheaper to make native PCI-E cards. Doubble the speed even though you wont notice it for a while.
And for graphics card's, what do you want to do with this PC?