The only drawback, which makes this a strange deciding factor, is that the PCIe version of the GF6800 isn't modable, but the AGP version is quite often modable. It's a consideration if you're more interested in that then not having to replace your motherboard in the future. But it's damn hard ot recommend a new AGP board to anyone, because it does have a limited opportunity lifespan IMO.
However if he's not upgrading for a year or two it may have little impact anyways because by that time it's likely that there will be the shift to different sockets and memory, as well as other features.
Just a thought.
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Since you haven't bought the mobo yet, I'd recommend going PCI-e and ATI. For $20 more(in the USA anyway) than a GF6800 PCI-e, you can get a <A HREF="http://www.monarchcomputer.com/Merchant2/merchant.mv?Sc..." target="_new">X800XL 256MB</A> which is far superior. Or you could save money and get a X800 128MB for $150 or so. Of course outside the USA things could be different.
GF6600GT and GF6800 are not bad options in AGP, but IMO ATI rules the $150-$250 PCI-e market right now. EDIT: Shoot, why not make that $150-$300+. It's not until $330 or so that a 6800GT can be bought, and even then hard to justify one <A HREF="http://www.newegg.com/Product/Product.asp?Item=N82E1681..." target="_new">given the XL's price</A>. I'd go with the HIS for $288 with its vga silencer and Flatout game.