The MSDN documentation on Web.Config Transformation does not really help regarding generating the transformed config files in Visual Studio 2010, without going though full publications and involving the other solution projects.
For generating the most low-impact Transform operation outsite Visual Studio you have to add the following to your C:\Program Files (x86)\MSBuild\Microsoft\VisualStudio\v10.0\WebApplications\Microsoft.WebApplication.targets and call msbuild with the task as \target, this could be put as a post build event, this way you can always check that your configuration transformations are merged as expected instead of having to guess, otherwise a fantastic new feature in the framework.
call "msbuild" "D:\Solutions\Intranet.Web.csproj" /t:Transform /p:Configuration=Release
You can also add it to the *.csproj file but it would be removed by VS upon editing, the other file is included by VS into the csproj.
1: <UsingTask TaskName="TransformXml" AssemblyFile="$(MSBuildExtensionsPath)\Microsoft\VisualStudio\v10.0\Web\Microsoft.Web.Publishing.Tasks.dll" />
2: <Target Name="Transform">
3: <MakeDir Directories="obj\$(Configuration)" Condition="!Exists('obj\$(Configuration)')" />
4: <TransformXml Source="Web.Config" Transform="Web.$(Configuration).config" Destination="obj\$(Configuration)\Web.config" StackTrace="true" />
5: </Target>