We started down the path of DotNetNuke and some commerce modules, but in the end it was easier to just code it ourselves.  Although very powerful, the DNN commerce modules were just too limiting.

We’re using C#, ASP.NET, and SQL Server 2005.  They already have an Authorize.net account, so the credit card processing is very easy through their API.  The store supports features such as pricing matrix, related products, out-of-stock messages, shipping, tax, filtering the products by the registered user’s state of licensing, and full integration into their CRM system.