M.2 slots are already available on a couple of desktop motherboards. Next year, we could see them on a lot more. An official-looking specification list posted on HKEPC suggests that Intel's 9-series chipsets will officially support the mini SSD standard. The spec sheet includes details for the Z97 and H87 platform hubs, both of which will reportedly have a single M.2 connector tied to dual PCI Express lanes. Although the slide isn't specific, that PCIe connectivity will likely be of the Gen2 variety. Both chipsets are shown with eight lanes of PCIe 2.0.
Chipset support for M.2 SSDs isn't explicitly necessary, of course. Plenty of notebooks based on Intel's 8-series platforms already use M.2 SSDs. Asus' Z87-based Maximus VI Extreme desktop motherboard also has an M.2 slot, and ASRock just announced a Socket AM3 board with one, as well. The ASRock offering is the first two-lane implementation we've seen on a desktop board, and it looks like that configuration will be the standard for Intel's 9-series chipsets.
Two lanes are better than one, of course, and SSDs can already take advantage of the additional bandwidth. This summer, Samsung introduced an M.2 drive whose 1400MB/s peak sequential read rate is fast enough to saturate a two-lane PCIe 2.0 link. That drive has a four-lane M.2 interface, and so does SandForce's next-gen SF3700 controller, so I'm a little surprised that the Z97's M.2 connectivity appears to be limited to a single x2 link. Then again, I can't think of any desktop applications that require disk transfer rates higher than the ~1GB/s offered by dual PCIe 2.0 lanes. If mobo makers already provide M.2 slots without official chipset-level support, I suspect they'll be able to graft M.2 x4 slots to Intel's 9-series chipsets.