I imagine, it might depend largely on what you're specifically looking for: configurability, design, turn-key readiness, drop-ship integration, sales tax automation, responsive support etc. If you have a preferred payment gateway or would like to use your own custom SSL cert, that will impact your choices as well. In the meantime, take a look at Volution, Bigcommerce, Corecommerce, Squarespace, Big Cartel, and Storenvy. If you're looking to build something in-house: check out SpreeCommerce and Magento.