The 128Mb card running 1000MHz video ram should outperform the 256Mb card running 900MHz video RAM. If you are after pure speed, then that's the deciding factor.
If, on the other hand, you are going to be insistent on running the highest graphical details you can possibly put on screen, regardless of whether or not it causes slowdows, then the extra video RAM would help with the massive texture calculations.
I agree with cat weasle. However, both provide great overclocking abilities if you want to follow that route, more so the 6600 GT / 128MB DDR3. Looking at speed when overclocked a 6600 GT / 128MB DDR3 can perform much like a regular 6800 which is useful, i'm thinking of buying one of these myself and saw both cards and pondered about which one I should buy but i gave into the 6600 GT / 128MB DDR3 mainly because not even the highest of demanding games need 256mb to give a good game, its all about fluidity. I hope this is of any help and hope you havent made any bad purchases yet cause the 6600 GT / 128MB DDR3 is a clear winner in my books.