Microsoft.WebApplication.targets was not found, on the build server. What’s your solution?

To answer the title of the question (but not the question about the output you’re getting):

Copying the following folder from your dev machine to your build server fixes this if it’s just web applications

C:\Program Files (x86)\MSBuild\Microsoft\VisualStudio\v10.0\WebApplications

Remove x86 according to how your build breaks. If you have other project types you will probably need to copy the entire msbuild folder.