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shopping carts are also often separate from the e-commerce system, and they need to be tied together. it's fairly easy to integrate your site / shopping cart system with card processing services such as worldpay, 2checkout, netbanx and others.
if you can give us more information, we can give you more information. do you have a site online now? what type of server are you on? (some carts will only run on windows, others only on *nix etc). how many products will you be selling and will there be any special requirements like different shipping casts to different parts of the world and so on? (not all carts can handle these things). anything else that we might need to know? the more information you can give, the better people can help.
if you want to sticky mail me with your URL or put it in your profile, i can take a look and suggest some carts or whatever you need.
It all depends on how you want your website to integrate with the cart.
Do you just want to have a "Store" link in the navigation?
Or do you want to have product links within, say product or category reviews pages which exist on your current website?
The hyperlink is a mighty tool. Wield it wisely.