Assuming your motherboard supports nVidia SLI, I think two 6600 GT's will be faster than one 6800 GS. According to this review
http://techreport.com/reviews/2005q1/geforce6600gt-sli/index.x?pg=1it looks to be about 20-40% faster than a single 6800GT (which is about as fast as a single 6800GS). Power consumption and heat generation will be twice as high as with a single 6600GT, so you'll need a good power supply (my guess is 500W or higher) and keep an eye on cooling (might want to use RivaTuner to make sure your GPU's at least don't overheat).
I don't know if there is any issue with two SLI cards not being exactly the same (such as if you have one that is from one manufacturer and one is from another manufacturer who has the GPU clock set slightly differently, or whatever). I suppose you could use RivaTuner to make the settings for the two cards to be the least common denominator.
Since all the newer 6800GS cards are decently overclocked from the factory, a current 6800GS is probably faster than the 6800GT's or 6800GS's used in reviews that are a year or more old (as those are probably not overclocked).
As for price, 6600GT's seem to be about $140-$150 and 6800GS's seem to be about $180-$200 (at least from newegg.com). I've had good luck with an XFX card and back luck with several eVGA cards, in case you are interested in which brands to try.