Well, with the exception of a few models, all motherboards will support either AGP or PCI-E, and not both. While the difference between the two cards is not hugely significant, i'd still go with the PCI-E card if you have the option. The performance is somewhat better, and you have far greater upgrading potential.
Without getting into the technical details, PCI-E has a higher bandwidth than AGP, and thus can transfer data faster. PCI-E cards are generally cheaper than similar AGP ones, and modern high-end cards are now PCI-E only.
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CPU: Core 2 Duo E6600 / MOBO: Gigabyte 965P-DS3 / GPU: Gigabyte HD4870
RAM: 2GB G.Skill F2-6400CL4D-2GBPK / HDD: 2TB Total HDD / PSU: Antec NeoPower 480W
Cheap PSUs - 2% of system costs, responsible for 28% of system deaths As Sealed Stick was removed, lost or damaged, it shall be out of warranty validity. - The "Warranty void if removed" sticker on numerous CoolerMaster PSUs.
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