Question: Is there a difference between PCI n AGP graphics card in terms of performance? 

Answer: Yes there is.  Not only is the AGP bus technology more advanced than PCI, the video cards available for AGP slots are generally alot faster/better than ones available for PCI slots.  For example, in the previous generation of video cards the most powerful nvidia PCI video card was the FX5500 while the most powerful nvidia AGP video card was the FX5900 (higher model numbers are better than lower ones).  With the current generation of video cards, I don't even think any PCI versions are available.
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