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I would go for the PCI-e if you're going to upgrade. The 7800 GTX is only offered in PCI-e right? The video card companies have made the jump, so should you. I think AGP and PCI-e based cards are pumping out similar benchmarks, so you won't be losing any graphical power by making the jump.
Good luck.
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Desktop 1: Intel i7 920--GA-x58-UD3R--Corsair xMS3 6GB (3 X 2GB) DDR3 1333mhz--Sapphire HD 4870 1GB--PC Power & Cooling Silencer 750w psu--WD SATA 3.0 gb/s 320 GB HD--Lite-on DVD-DL burner--Thermaltake SopranoRS black case--Windows 7 Professional 64-bit
Desktop 2: Intel C2D E4400--GA-P35-DS3R--Corsair xMS2 2GB (2 X 1 GB) DDR2 800--eVGA 8600 GT--Fortron Source 500 watt psu--WD 250 gb HD--HP DVD-DL burner--Windows Vista Home Premium
Laptop: Apple Macbook
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