The Jetway NF81 has an AMD Fusion APU which should take care of your HD graphics needs, and it has a standard mPCIe and an mSATA port. There's also a nano-itx board with Fusion/mPCIe/mSATA but it's not available yet. Intel's NUC could be an option later this summer, but anything smaller than Mini-ITX is going to have onboard power, not ATX.
The physical interface for mSATA and mini PCIe are identical; the difference is in the signaling. So, you cannot use a mPCIe wifi card in an mSATA port, or an SSD in a mPCIe slot (unless it's actually a mPCIe SSD, which is possible). There are actually three different signaling conventions for storage devices using the same mPCIe interface, mSATA, or USB. mSATA is the most straightforward and will hopefully become the default with Intel pushing it. There are also some proprietary systems out there used by laptop manufacturers, and those vary in both the length of the card and the signaling.