Alrighty, lets see here. How about making the Motherboard a different Shape? Or even have the placement of the North/Southbridge different than the standard motherboard. The "Neo 2 Platinum" from MSI nearly had it when the ram was situated above the CPU. Re situating everything might even lead to performance increases for all you know, and on top of that it'll add to the look being a "Unique" board.
2 - Like others have said, remove the pointless things. No, we don't want Firewire, no we don't want IDE, etc. Make it USB3 compatible of course, Esata, and a must is that ALL ports have to be PCIe 16, no more "PCI" slots. PCIe is the future.
3 - Back to cosmetics, like previously stated light up the slots. Simple LED's, Red LEDS light up the slots that aren't in use and Blue light up the slots in use. (or w/e color best suited for you). Lights lights and more lights is where its at. But, add an option to remove the lighting so that those who want a dark moment for a game can toggle the lighting off.
Make it support both ATV and nVidia of course, Support the top speed DDR3 Ram, make it support the socket 1336 (so for future I9's).
To clear the clutter of cables, the power connections should be either near the top, on the right edge (very edge) or on the very bottom.
The Northbridge/Southbridge heatsinks of course need to be flashy. So make them large, and colored to create that whole feeling of epic.
On board OC'ing, on board bios reset, reset, power, etc. LED display on the board to display current temperatures, clocks, power consumption.
And to top the cake, make the bios flashy. Not the basic "blue with yellow words". If possible, make it designed, so when you're in there OC'ing and people are watching it looks good.