If you want something free then Magento (http://www.magentocommerce.com/) or Zen Cart (http://www.zen-cart.com/) If you are ready to pay then jStore (http://www.ijoobi.com/)
Zen cart is good for a free cart, but do yourself a favor and pay for the cs-cart or bigcommerce. Zen cart DOES NOT have built in SEO features AT ALL and the simple SEO URL mod kills your disk space usage (it is necessary for SEO URL's). CS-Cart also has a built in affiliate system, auto product uploads, and several on-page optimized options built in. You will have to pay extra or spend some time to create a customized theme, but what you pay up front will save you tons of hassle and headache down the line. Stay away from zen-cart unless you are on a shoestring budget. I have also heard awesome things about bigcommerce, but I don't think you can host it on your own server. It also depends on if you need to host it on your own server or not, what your budget is, how many items you plan to carry, hosting options (dedicated or shared), and a variety of other questions. Lots of variables when it comes to shopping cart scripts.
IMHO both Prestashop & Magento are nice. It depends on your need, a simple one (Prestashop) or the more advance one (Magento)
I would like to recommend AJ Shopping cart which is best and more affordable to buy. I am running my online shop successfully using aj shopping cart. Try it now. http://www.ajsquare.com/products/ecom/index.php
You're asking the wrong question. There are plenty of good shopping carts out there and the "best" is often nothing more than a matter of taste, preference, or at best dependent on your individual needs and concerns. The better question is "which shopping carts should I avoid at all costs" And for that my vote goes to Shop Factory.