It totally depends on the location of your business, the type of your shop, etc. Oscommerce provides the most comprehensive solutions, paypal is not supported in some countries. I am trying Wp-ecommerce. They are nice despite some concerns about security.
Wassim (here in dp) developed a very cool flash shopping cart .. check it The cart comes in two flavors, an XML driven version and a MySQL+php adminPanel powered version;
magento, it has so many features and is really organized (maybe too much?). only problem is that magento needs a lot of resources. anything less than a vps will make your magento site crawl.
I have used paypal as my shopping cart since 2007, it has a decent amount of features for a small fee for each transaction. You have the option of customizing your buttons and checkout page as well to a certain extent. It does have a few issues though I can speak of, such as holding your funds for what appears to be no reason and recently reviewing high cost transactions (usually holding funds for up to 24 hours). I would say it works great for small companies. If you have a large inventory I would recommend using one of the previously listed carts.
Viart. I have used it for multiple sites and it is great. Limited templates but good ones. The software is very good. My main complaint is that they are located in Europe so if you do business in the US it can take a while to get issues resolved with one email and one response each night.