a quick google found HardOCP Looking at a 6600GT "SLI" card produced by gigabyte...
OK, it's not actually 2x6600GT cards in SLI, but this single card is effectively the same, and should perform as such.
That review shows that the 2x6600GT cards being roughly the same as a 6800GT (SLI better in DOOMIII, everything else the single 6800GT is better). I know that's not a GS, but the 6800GT and GS perform at very similar levels, so it's a reasonable indicator of performance.
Based on that, I'd definitely say to go with the 6800GS solution. It's a less complicated solution, and you won't have to worry about driver profiles/SLI-quirks robbing you of half your performance in the odd game here and there.... Plus the 6800GS (PCI-E at least) overclocks like a beast.... And I bet at the (very reasonable expectation) 20% overclock it'll thrash the Sli config easily.