Hold out a little while longer for mobos with PCI-X slots. AGP is about to go the way of the dodo. It's not the best time to invest in a new board and new expensive AGP card, trust me.
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I don't much reckon that PCI-E will be a standard in every computer until at least this time next year, so really, there's still a year's worth of time where a moderately priced AGP card (say 9600-9800) running on a relatively cheap motherboard with AGP 8x (my board cost ~£40, works perfectly) just to bide your time until "true" PCI-E cards are released and the cost of new technology drops.
PCI-X is completly useless at the momment. AGP will not be replaced for at least 2-3 years. We barely even use AGP 8X now.
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PCI-E is running great as it is, and yes, 8x AGP is being used. What you're talking of is the fact that graphics cards are not utilising PCI-E slots to their full potential. That's true. Right now i don't think there is a "true" PCI-E video card on the market, i could well be wrong, but cards such as the 6800 are "bridged" PCI-E, which is basically just a cheap hack and offers little to no gain over it's AGP counterpart. The reason for the bridging is so you can buy a motherboard with PCI-E, which won't have AGP, and still be able to run a graphics card.
Yeah, the PCI Express cards aren't improving much over the regular AGP ones right now. But like Bob said, they will later.
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Bingo.