I think I have actually seen this error in other versions of TFS besides 2010, but most recently saw it in 2010 deployment. Post-executing build configuration when running a build for something using Web Application projects you might receive the error:
The imported project “C:\Program Files\MSBuild\Microsoft\VisualStudio\v10.0\WebApplications\Microsoft.WebApplication.targets” was not found
To solve this issue, just copy the C:\Program Files\MSBuild\Microsoft\Visual Studio\v10.0\WebApplications directory from a development machine to the build machine. Sucks but it works. Seems sporadic why it happens.