Are you buying the micro or low profile cases? If so, then the half length means that only short PCI cards like modems and NICs will fit into that slot. Something giant like a VooDoo2 or V5-5500 will not fit in there.
It's not the size of the PCI slot, it's more the lenght of the PCB of the card.
I buy the GX110 towers. Damn nice machines.