The X58 boards are one such example...It has 40 PCIe lanes, out of which it allocates 36 PCIe lanes for the PCIe x16 slots and the rest are used for other components...
So most of the boards vendors, allocate full x16x16 lanes when only 2 cards are populated but this is not the case for some boards like the EVGA 141-BL-E757-TR LGA 1366 Intel X58 ATX X58 SLI LE , where the PCIe slots are set to run X16 x8 even when only 2 cards are populated...So that is the mistake of the mobo manufacturer...