I'm surprised no one has mentioned using T4 to generate the WXS file during build. I learned about this by way of Henry Lee @ New Age Solutions.
Essentially, you create a custom MSBuild task to execute a T4 template, and that template outputs the WXS just before the Wix project is compiled. This allows you to (depending on how you implement it) automatically include all assemblies output from compiling another solution (meaning that you no longer have to edit the wxs ever time you add a new assembly).
