What version of .NET comes with Windows Server 2008

As mention, the .net framework is now an integral part of the OS and can't just be repaired from add/remove programs. You can run System File Checker, to check the OS components by running this from the command prompt.

sfc /scannow

However the only way to perform a full repair of the .net components is to repair or re-install the OS.

By default, Windows 7 and Windows Server 2008 comes with .net 2.0 and .net 3.5. Remember even though you have .net framework 3.5 the CLR version is 2.0. There is no CLR v3.5. You can always host .net 3.5 related applications on the server where your web.config file will be referencing the necessary namespaces.

From the article .NET Framework 3.5 Architecture

The architecture of the .NET Framework version 3.5 and 3.5 Service Pack 1 (SP1) builds upon the earlier versions of the .NET Framework.

An application uses the same assemblies regardless of whether it targets the .NET Framework version 2.0, 3.0, 3.5, or the Client Profile, and regardless of whether the assemblies have been updated on a user's computer. For example, an application that uses Windows Presentation Foundation (WPF) and targets the .NET Framework 3.0 uses the same instance of the mscorlib assembly as an application that uses Windows Forms and targets the .NET Framework 2.0.