Most of our clients with ecom sites use InSynch from ROI-Consulting as the engine for integration. Some have developed their own shopping carts for use with InSynch while with others we have used one of the more out-of-the-box shopping carts for integration. Pretty sure WebSite Pipeline uses InSynch as well, or at least they used to. Avatax has a connector for most common shopping carts and maybe can create one for custom carts.