.NET 3.5 is essentially 2.0 with a few extra libraries. The answer is, yes -
you can run them on the same web site. In fact you cannot set a web application
to run under 3.5. It just runs under either 2.0 or 4.0. You can check
the ASP.NET tab in the properties of an IIS site to see your options. As long
as your server has 3.5 installed, you can run both.
You can run code in .NET 2.0 and .NET 3.5 on the same server, but you must
have at least one application pool per framework version. The only thing you
have to watch is not to mix a 2.0 app and a 3.5 app in the same application pool.