The relationships between the .NET
Framework versions 2.0, 3.0, and 3.5
differs from the relationships between
versions 1.0, 1.1, and 2.0. The .NET
Framework 1.0, 1.1, and 2.0 are
completely separate from one another,
and one version can be present on a
computer regardless of whether the
other versions are present. When
versions 1.0, 1.1, and 2.0 are on the
same computer, each version has its
own common language runtime, class
libraries, compiler, and so forth.
Application developers can choose
which version to target. For more
information, see Side-by-Side
Execution, Targeting a Specific .NET
Framework Version or Profile, and
Using MSBuild to Target Specific
Versions of the .NET Framework.
link
O .NET 4.0 também é uma versão nova e isolada que pode ser executada ao lado de qualquer uma das outras sem interferências.