In the lower end, with average / slow single drives, etc., it doesn't matter much. If you're trying to push the performance to the high end, it's better to stay away from PCI GbE NICs, and especially the combination of PCI GbE + PCI storage controller on the shared PCI bus. (Exceptions for higher-end servers with PCI-X, etc.)
With PCI NICs, it helps to have jumbo frame support (typically relatively more than it helps PCIe / good on-board solutions).