One problem I had with this was for the live deployment. Although the configuration transforms were working great for publishing, for the live environment we also wanted to apply the minify tasks to the CSS and JavaScript files (See my other post on post build tasks and minification).
Web Deployment Projects
Currently, web deployment projects don't apply the configuration transforms, so I had to find another way to apply this. Since I already had post build tasks in place for the minification, I figured this was the way to go to apply the transformations. After finding this question I was almost there.
Using the above post, I was able to identify the task used to transform the configuration files in the V10.0 publishing assembly. Unfortunately once the task has run it leaves the files locked by the process so in addition I had to add a couple of additional tasks to copy the files to a temporary location first, and copy back across to the project folder when done. Once this was complete I setup a task to delete the redundant files for other build configurations and remove the temporary file if possible (the temp file appeared to still be locked by the process so may not delete in some cases. However, this directory will be overwritten by the standard process the next time you build anyway).
The build task configuration is below. If you right click on the web deployment project and select 'Open Project File' you should be able to paste this in at the bottom (I have excluded the Minify task for brevity).
<UsingTask TaskName="TransformXml" AssemblyFile="$(MSBuildExtensionsPath)\Microsoft\VisualStudio\v10.0\Web\Microsoft.Web.Publishing.Tasks.dll" />
<Target Name="AfterBuild">
<!-- Copy the config transform file to a temp directory (to stop it being locked by the process) -->
<Copy SourceFiles="$(Configuration)\web.$(Configuration).config" DestinationFolder="TempBuildDir\" />
<!-- Delete the config files from the deploy folder (to be replaced by the transformed files) -->
<ItemGroup><ConfigFiles Include="$(Configuration)\\**\*.*.config" /></ItemGroup>
<Delete Files="@(ConfigFiles)" />
<!-- Transform the copied files and write to the deploy folder -->
<TransformXml Source="$(SourceWebPhysicalPath)\Web.Config" Transform="TempBuildDir\Web.$(Configuration).config" Destination="$(Configuration)\Web.config" StackTrace="true" />
<!--Then remove the temp files folder (locked by the transform process...)-->
<RemoveDir Directories="TempBuildDir\" ContinueOnError="true" />
</Target>
Conclusion
This enables the web deployment project to build the website with the correct configuration AND minified JavaScript and CSS files. I can then build the package and distribute via the web deploy tool in IIS7.