Right now I use Miva Merchant: http://www.mivamerchant.com
, I'm looking at other carts, 3d Cart is one of them, unfortunately starting out with 3d Cart there are some 'issues' I do not like to see, 1.) Cookies required to add product to cart, 2.) common 'options' do not work, 3.) some design issues do not work properly.
Because of those problems I'm looking at other carts as well. Miva Merchant is the oldest Shopping Cart around, as far as I know. You can do just about anything you want with it, but the most important part, you have to be able to do the 'right things' required to help you gain sales, such as offer Single Landing Pages, Discount Coupons, Loyalty (reward points), Reminder Emails, Custom Account Profiles, Shipping Options that work as advertised, Order Management (to cut your time down managing the cart), Inventory Management, etc, etc....
It really depends on what you want to sell, selling Digital Products (eBooks, or Software) is a whole different ball-game from selling Physical Products, from selling Services, so far Miva Merchant is the most feature rich cart ever, unfortunately it's a bit pricey, but if you're serious about your online business you would be wise to consult with someone first, get your ideas/products setup the way you want and go from there.