Have a look at our new add-on to Whidbey: Web Deployment projects. From the overview:
A Web Deployment Project creates and maintains an MSBuild project file, and is associated in a solution with a Web site project. A Web Deployment Project enables you to manage not only build configuration and merge options, but other tasks such as specifying changes for the application's Web.config file during compilation, changing connection strings, creating virtual directories, and performing other tasks at specific points in the deployment process.
The new assembly merge tool (Aspnet_merge.exe) combines assemblies created during ASP.NET 2.0 precompilation for deployment. The tool supports many merge options, from combining assemblies for each Web site folder to creating a single assembly for the entire Web site.
Here is link to documentation.