Having a way to designate one of the signals as a clock and registering the other signals would be a great addition for sniffing higher speed synchronous buses such as JTAG or SPI, even DDR SDRAM. This would allow capturing 2x to 4x faster clock rates than is currently feasible because you only need to record one sample per clock, not 4 or more.
For some things, it's also easier to just see it from the point of view of what was registered on the bus, without worrying about exactly when. It's a little-bit higher level.
Now that you have that spiffy Spartan-6, let's put it to work! It should be fairly straight-forward to use its IO resources, DDR flip-flops and clock muxes to select a clock and to register the other signals.