Microsoft.SharePoint.Publishing: This is the Publishing DLL. All the functionality from CMS 2oo2 has been brought with this DLL into MOSS. Also some new functionality has been added into this.
Microsoft.Office.Server: This DLL is available only with MOSS and will not be available with WSS. Includes overlapping functionality with Microsoft.SharePoint.dll but with some refinement. It also includes functionality specific to MOSS such as BDC, reports, etc.
Microsoft.Office.Policy/Microsoft.Office.Workflow: These DLL helps for the Document Life Cycle part of the and for document management and workflows.
Microsoft.SharePoint.Search: this is the Search functionality corresponding to WSS Search.
Microsoft.SharePoint.* : traditional namespaces from v2 with added classes and method references.