Easily the biggest feature of the MSI K8N Neo3-F is its support for 8xAGP videocards. The AGR slot, as MSI likes to call it, runs through the PCI Express bus although MSI does not state exactly how quickly data travels (I'd guess it's PCI express x2 - but don't quote me on that).
In any case it should be faster than competing PCIe/AGPe boards where the ersatz AGP slot (often called AGPexpress) runs through the standard PCI bus.
Unfortunately though, the videocard you wish to use must be pre-approved by MSI otherwise it will not function in the motherboard. PCstats test Asus X800 XT PE videocard would not run with the K8N Neo3-F motherboard but a MSI GeForce 4 Ti4800 worked just fine. The list is rather large, but requiring a pre-approved videocard ultimately defeats the purpose of the AGR slot.
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So, yes, you can use either. Due to the compatibility issues, I'd recommend a true PCI-Express video card.
You will need a proper ATX 2.0 power supply with a 24 pin connector to handle a PCI-E video card, especially a power-hungry one, factor that into your decision if you are running an older 20 pin unit. Dual +12v rail units are preferred. If you don't want to do this, go for a higher power AGP card, but make sure it's on the MSI approved list.
http://www.msi.com.tw/html/products/...f/7135/vga.pdf