This is another great question, Severus! I wouldn't really recommend specifically going out and buying a board that is capable of running multi-GPUs in x16 mode, as the performance benefits really aren't that great.
If we were talking PCIe 3.0 hardware, and some multi-monitor, multi-GPU gaming, maybe... but even then, we're talking less than 10-percent improvements across the board, most like 4- to 5-percent improvements. If you haven't already bought the GPUs (you say you're buying a new desktop PC) then I would save the money and get a board that doesn't cost that much (all boards have a single x16 port at least) and spend the money from the two GPUs on one single, faster GPU.
This way, you could get something like a ZOTAC GeForce GTX 670 for just $399.99 from Newegg. GeForce GTX 560's are still around $170 each, meaning a single GPU is only a bit more, but you do gain more performance from a single GPU, and less troubles with scaling and game compatibility, as well as not needing to worry about SLI for now.
Then, when you're ready for SLI, your motherboard will handle dual x8 ports, and you can throw another GTX 670 in it for some serious horse power.
Image is courtesy of Tech Support Guy, I thought it explained it well showing the bandwidth and all.