How to specify different nuget package versions for different build configurations?

This is not supported as far as I am aware with the packages.config file. You can only have one NuGet package with a specific id in a single project's packages.config file.

You can have different NuGet packages if you have different projects all sharing the same source files. This approach is typically used by library authors who have platform specific projects that need different NuGet packages. The project files can all live in the same directory with a packages.config file named after the project (e.g. packages.MyProject.config).

It may be simpler to not use NuGet to add the assemblies to your project. Just use NuGet to download the packages using nuget install and then directly reference the assemblies you need with conditions.

This is totally supported by MSBuild, although Visual Studio has no built-in support for it, so it requires some hand editing. We did this on the MvcSiteMapProvider project to support MVC versions 2-5.

  <ItemGroup Condition=" $(DefineConstants.Contains('MVC2')) ">
    <Reference Include="System.Web.Mvc, Version=2.0.0.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35, processorArchitecture=MSIL" />
  </ItemGroup>
  <ItemGroup Condition=" $(DefineConstants.Contains('MVC3')) ">
    <!-- Due to the windows update MS14-059, we need this hack to ensure we can build MVC3 both on machines that have the update and those that don't -->
    <Reference Condition=" Exists('$(windir)\Microsoft.NET\assembly\GAC_MSIL\System.Web.Mvc\v4.0_3.0.0.0__31bf3856ad364e35\System.Web.Mvc.dll') " Include="System.Web.Mvc, Version=3.0.0.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35, processorArchitecture=MSIL" />
    <Reference Condition=" !Exists('$(windir)\Microsoft.NET\assembly\GAC_MSIL\System.Web.Mvc\v4.0_3.0.0.0__31bf3856ad364e35\System.Web.Mvc.dll') " Include="System.Web.Mvc, Version=3.0.0.1, Culture=neutral, PublicKeyToken=31bf3856ad364e35, processorArchitecture=MSIL">
      <Private>True</Private>
      <HintPath>..\packages\Microsoft.AspNet.Mvc.3.0.20105.1\lib\net40\System.Web.Mvc.dll</HintPath>
    </Reference>
    <Reference Include="System.Web.Razor, Version=1.0.0.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35, processorArchitecture=MSIL">
      <Private>True</Private>
      <HintPath>..\packages\Microsoft.AspNet.Razor.1.0.20105.408\lib\net40\System.Web.Razor.dll</HintPath>
    </Reference>
    <Reference Include="System.Web.WebPages.Razor, Version=1.0.0.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35, processorArchitecture=MSIL">
      <Private>True</Private>
      <HintPath>..\packages\Microsoft.AspNet.WebPages.1.0.20105.408\lib\net40\System.Web.WebPages.Razor.dll</HintPath>
    </Reference>
  </ItemGroup>
  <ItemGroup Condition=" $(DefineConstants.Contains('MVC4')) ">
    <Reference Include="System.Web.Mvc, Version=4.0.0.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35, processorArchitecture=MSIL">
      <Private>True</Private>
      <HintPath>..\packages\Microsoft.AspNet.Mvc.4.0.20710.0\lib\net40\System.Web.Mvc.dll</HintPath>
    </Reference>
    <Reference Include="System.Web.Razor, Version=2.0.0.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35, processorArchitecture=MSIL">
      <Private>True</Private>
      <HintPath>..\packages\Microsoft.AspNet.Razor.4.0.20715.0\lib\net40\System.Web.Razor.dll</HintPath>
    </Reference>
    <Reference Include="System.Web.WebPages.Razor, Version=2.0.0.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35, processorArchitecture=MSIL">
      <Private>True</Private>
      <HintPath>..\packages\Microsoft.AspNet.WebPages.4.0.20710.0\lib\net40\System.Web.WebPages.Razor.dll</HintPath>
    </Reference>
  </ItemGroup>
  <ItemGroup Condition=" $(DefineConstants.Contains('MVC5')) ">
    <Reference Include="System.Web.Mvc, Version=5.0.0.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35, processorArchitecture=MSIL">
      <Private>True</Private>
      <HintPath>..\packages\Microsoft.AspNet.Mvc.5.0.0\lib\net45\System.Web.Mvc.dll</HintPath>
    </Reference>
    <Reference Include="System.Web.Razor, Version=3.0.0.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35, processorArchitecture=MSIL">
      <Private>True</Private>
      <HintPath>..\packages\Microsoft.AspNet.Razor.3.0.0\lib\net45\System.Web.Razor.dll</HintPath>
    </Reference>
    <Reference Include="System.Web.WebPages, Version=3.0.0.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35, processorArchitecture=MSIL">
      <Private>True</Private>
      <HintPath>..\packages\Microsoft.AspNet.WebPages.3.0.0\lib\net45\System.Web.WebPages.dll</HintPath>
    </Reference>
    <Reference Include="System.Web.WebPages.Razor, Version=3.0.0.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35, processorArchitecture=MSIL">
      <Private>True</Private>
      <HintPath>..\packages\Microsoft.AspNet.WebPages.3.0.0\lib\net45\System.Web.WebPages.Razor.dll</HintPath>
    </Reference>
  </ItemGroup>

You can't use the NuGet package manager, either. You can create different dummy projects for each configuration you want to support, install the NuGet packages there and then copy over the packages files, the references in packages.config, and the references to them in the .csproj or .vbproj file.

The non-active files show up with a yellow icon, but the project will still compile and run this way.