The 1200 is bigger. You get 12 drive bays instead of 9. That's why the names 1200 and 900, btw. Mind you, with motherboards limited at 8 SATA ports I'm not sure who would need all those bays. It might help also if future video cards are even bigger than the 9800GX2.
Actually the HDD cages are longer by an inch or so, so there is not much of a difference between the 2 when it comes to fitting GPUs in them.