Commerce Server 2007 is Microsoft’s premier server for creating e-commerce solutions, building on over 10 years of innovation and success.
Traditionally, Commerce Server handles all commerce-type transactions, e.g. shopping carts, product catalogs, inventory, order management, etc.
MOSS picks up where Commerce Server leaves off by putting forward web content management (versioning of product information, approval workflows), some level of collaboration (e.g. product review sub-sites) and generally handling the overall branding and management of the portal.
Since both products leverage on ASP.NET 2.0, they integrate really nicely together. Kind of like building an eCommerce site on steroids
E-commerce sites need to be part of a company’s overall line-of-business systems. By providing advanced integration features, Commerce Server 2007 makes such integration easier than ever. Specifically, Commerce Server 2007 will help enterprises:

• Connect seamlessly to internal and partner applications and systems such as SAP, Microsoft Dynamics, JD Edwards, and others through Microsoft BizTalk Server adapters. Commerce Server 2007 provides profile, order, inventory, and catalog subsystem adapters for BizTalk Server to accelerate and automate the delivery of products and services.
• Manage and share business data through industry-standard Web Simple Object Access Protocol (SOAP) Extensible Markup Language (XML) protocols. All core subsystems are Web-service enabled to facilitate business data management and updates.
• Provide customers and partners with Web-based self-service through access to order status and inventory availability, wish lists, and order change management.
• Exchange and aggregate product catalog information from across your business and from trading partners to present expanded product and service line offerings.