How can I exclude a project from a build in MSBuild?

In your solution file (.sln), remove the Build.0 entries. For example:

Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "MyProject", "MyProject.vcxproj", "{2281D9E7-5261-433D-BB04-176A61500CA3}"
EndProject

GlobalSection(ProjectConfigurationPlatforms) = postSolution
    {2281D9E7-5261-433D-BB04-176A61500CA3}.Debug|x86.Build.0 = Debug|x64

If you delete this "Build.0" entry, it will load in the solution fine, but will not be built, either through the GUI or via external MSBuild.

You can exclude projects at the solution level for a specific build configuration by using the Configuration Manager Dialog in Visual Studio:

Then you can simply invoke msbuild on the solution file specifying the build configuration to use:

msbuild /property:Configuration=Release MySolution.sln

The solution suggested by Enrico is the most versatile solution that would work always. An alternative solution might be to use a <MSBuild> task directly. This will work for you if you have all your project files under a particular directory, or be able to easily enumerate all projects you want to build (i.e. number of projects in your solution is not very big).

For example, this MSBuild file will build every project under your current directory except for a specific project:

<Project xmlns="http://schemas.microsoft.com/developer/msbuild/2003">

  <ItemGroup>
    <MyProjectReferences Include="**\*.*proj" />
    <MyProjectReferences Exclude="Utilities\DTS Indexing Service\Tdi.Origami.IndexUpdaterServiceSetup\Tdi.Origami.IndexUpdaterServiceSetup.wixproj" />
  </ItemGroup>

  <Target Name="BuildAllExceptWixProject">
    <MSBuild Projects="@(MyProjectReferences)" Targets="Build" />
  </Target>

</Project>

Then you can build that using command line msbuild <myproject> /t:BuildAllExceptWixProject