In my project I use NAnt to automate the entire regeneration and build process. I've gone down the route of customizing the NetTiers templates, but that only works until you decide you need the latest and greatest version from SVN. Unless you don't mind continually merging your custom changes with the latest version.
What I did instead, was use a perl script and Regex expressions to parse the generated .csproj files and add in the project references, after they are generated, and before they are compiled. It was a lot of work initially, but worth it now.
-Casey