Are you comparing the price of a motherboard alone to the price of a complete system with case, and with PCI-e, PCI, XORRO, SATA, IDE that the other do not have?
"PCI-e, PCI, XORRO, SATA, IDE" are just connectors and BUS. What makes the difference in a complete system is the hardware you connect to them. I'm still waiting for a complete X1000 HW configuration (drives, cards, and so) for a right price comparation with actual PCs.