The 6600 GT is just a slightly faster performer and a little better in terms of bang for the buck. It is available (like all cards of the Geforce 6xxx line) in both AGP and PCI-Express. You shouldn't have any problem though. It will run whatever you are playing now and whatever you play for the next two or three years.
FYI - PCI-Express is a new standard for various expansion and graphics cards. Although it is almost soully limited to graphics use at the moment, there are plans to try to introduce different typeds of cards (new USB and networking cards for example) in the future. AGP is showing it's age and reached all practical limitations as a graphics card format. The PCI-Express slots have a much larger bandwidth than AGP, allowing for quicker transfer of data. As a result of this new standard companies are phasing out or completely stopped making AGP graphics cards.
So the good news is you have a good graphics card that you should get a good bit of use out of and is suitable for what you do. The bad news is you will need to upgrade your computer or get a new one in two or three years time because finding an AGP graphics card will be as difficult as finding a regular PCI graphics card is today.
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