For more customized self-hosted solutions I tend to go with Zen Cart. Its open source, there’s a ton of plugins, and an extensive developer network for support. Lately though, I’ve become more interested in Magento. While I’ve heard the server load can be intense, the theme system looks very intuitive, and minor details (like mobile commerce support) make their application very attractive.

For small scale boutique sites I’ve come across a few hosted shopping cart solutions: E-Junkie, Shopify, and Foxycart. E-Junkie looks great except they offer no support for UPS shipping (a requirement for a recent client) and Shopify is fairly expensive for what you get (and you’re locked into their CMS system — which works for some people, but not for a web designer). I recently launched a site using Foxycart — a hosted solution charging a flat per-month fee. So far its worked great. The cart is easily customizable, works flawlessly with an Authorize.net gateway (and they use their own SSL certificate). Most importantly for this particular client, Foxycart supports automatic UPS shipping calculation and discounts over a certain price in a specific product category.