Another possible application: talking to high speed serial busses. This isn't just a Spartan 6, it's a Spartan 6 XCblahblahT. Usually when you see cheap Spartan 6 boards they use the non-transceiver version to cut costs without mentioning that it cuts one of the killer features of the chip! This one is the real deal. You still have to use ISE (not even Vivado; they locked the Spartan 6s out of Vivado) but it's still nice.
EDIT: they may have brought all the transceivers out to PCIe; I'd have to look closer to tell for sure.
This is MiniPCIe which would only have a x1 connection to the edge fingers, which means only 4 GTP connections would be needed (and the XC6SLX100T has 8 IIRC).
EDIT: they may have brought all the transceivers out to PCIe; I'd have to look closer to tell for sure.