I think with most MBs and cases it's more a question of whether the secondary slot you use supports 8x or 16x and whether using the farther one for spacing/cooling purposes allows expansion slot venting and PSU clearance, not to mention MB component clearance of those bottom ports you need to plug into for front panel, USB, etc. Regarding 8x vs 16x, it doesn't matter as much on modern Pci-Ex 3 MBs though because 8x on those is the same bandwidth as 16x on the Pci-Ex 2 ones.
A lot of people don't want to use the 2nd Pci-Ex slot, which typically has the 2nd GPU crammed right next to the first one, and with some so called dual slot GPUs, like Sapphire's 7000 series, the card shroud hangs out too far to even use the 2nd slot. My P6X58D-E MB is designed with a close 2nd slot and one near the bottom of the MB. I have clearance above my PSU and can even clear the small cables connected to the bottom of the MB if I don't use the Q-Connector, but my case has no exhaust slot on the expansion ports that low, and I'd have to buy a super long (like 120mm) bridge connector to connect the GPUs. The next MB I get will probably have a 2nd lost that is not right next to the first. I have to say using two video cards is more of a last upgrade resort for me though, and I've yet to bother with it.
TPU has done some Pci-Ex bandwidth tests comparing FPS between 8x and 16x slots on the old Pci-Ex 2 MBs when GPUs started exceeding 8x bandwidth, but as far as I know no such tests have been done since the 580 and 5870. If I recall correctly the 580 lost about 2% of it's FPS on 8x vs 16x. Again though, that is on Pci-Ex 2. On Pci-Ex 3 8x isn't an issue at all.
