There are two parts of the PCIe slot. One is the physical size of the slot, the other is how many lanes are electrically connected to that slot. The 16x means there are 3 full size PCIe slots on that motherboard. The x16/x16/x1 means the first slot will have the full 16 lanes connected, as will the second. The third slot will only have one lane, meaning that card will not be running as fast as it could. I can also appearently be set up to run 16 lanes on the primary card, with the second and third cards getting 8 lanes each.
16/16/1 is good for a two card SLi setup with the third slot running an Nvidia card as a PhysX card. 16x/8x/8x is better for a tri SLI setup. 16/16/4 is more like the first option, but with 4 lanes going to the PhysX card instead of just one. A 16x slot can run a 4x card, so this last one might be better if you want to run high end SATA/SCSI cards.