Most prefab carts are built to be stand-alone. Typically when you tie a cart like zencart to an existing site, you create a subweb (ex: /cart) or third-level domain (ex: cart.yourdomain.com), and modify the look of the cart to match your site. This is usually fine. But what if your existing site is a content management system with user registration? It would sure be nice to be able to integrate a cart that can work from the same system, along with other advantages associated with integration.
INTEGRATION SOLUTIONS
If you are using Joomla CMS, Virtue Mart is your obvious answer.
If you want to integrate into an existing custom design, webassit ecart and cartweaver are both good choices.
If you are using Modx cms (my favorite cms), Foxycart is the best solution.
If you are using WP, WP e-commerce is probably your best bet.
You can always make a quick n' dirty cart with paypal remote checkout. Of course, if you want to make a DIY cart for your client to add/update products this would not be recommended - unless you build a paypal local checkout system with webassist. Btw, webassist has made some nice improvements in their ecommerce with their new powerstore solution (making it much easier for novices).
There is quite a bit more that can be said on this topic, but thought I'd throw some solutions your way.
WebWeaver