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For one thing, I don't think that you can install aftermarket cooling on the AGP 6600GT due to the separate heatsink on the HSI bridge (for me, this is a large negative). The 6800 also preforms considerably better than the 6600GT, especially when AA gets enabled.
It may cost a little more but, in the end, I think that it's a better buy than the 6600GT.
the 6800nu is much better, especially an MSI, they're notoriously high quality boards. AGP still has all the bandwidth necessary so neither one is going to be bottlenecked by it. the 6800 has MUCH more throughput because of its 256bit wide memory bus. 22GB/s vs 16GB/s for the 6600GT
If you can you should try to find a 6800NU with the ddr3 memory... or even the 6800LE line (the lower than 6800NU version) w/ ddr3... a lot of sucess stories of getting those to GT speeds and ultra speeds, or better. Of course they'd have a big gap in price for the regular 256bit from ddr3 but if you find one for the price... jump on it
6800 NU much better then 6600 GT especially if ur lookin for AGP vers becuz then the 6600 gt is only like 20-30 more then the 6800nu and for that price, u get a much better performance.