PCI lanes determine how much data is able to transfer from the mobo to the components (GPUs and other accessory cards). If you have just one GPU in a slot then it will max out at 16 lanes. However, when you go for the multi-GPU setups you use way more lanes. With the X99 chipset boards, the setups you can have with just GPUs is 16; 16x16; 16x16x8; 16x8x8x8 (this is all if you have 40 lanes total). On the previous chipsets, 16; 8x8; 8x4x4; 4x4x4x4 would be the setups. If you do not use multiple GPUs then you can use the extra lanes you have for accessory PCIe cards like USB3.0 expansion cards. Every card you put in your mobo will use at least some lanes so if you have 4 GPUs (in 4 different slots using single GPU cards instead of dual GPU cards), then you will not have enough lanes.
Best analogy is like highway traffic. The more lanes the more data (cars) can travel unrestricted.