The Microsoft .NET Framework 3.0 (formerly WinFX), is the new managed code programming model for Windows. It combines the power of the .NET Framework 2.0 with new technologies for building applications that have visually compelling user experiences, seamless communication across technology boundaries, and the ability to support a wide range of business processes.
Also the .NET Framework 3.5 will still use the CLR 2.0. This new Framework - currently in beta 2 - builds incrementally on the new features added in the .NET Framework 3.0. Also new features will be added as new assemblies to avoid breaking changes.
Still not sure? Check it out for yourself : you can find the installed .NET Frameworks in \Windows\Microsoft.NET\Framework and via the CLRVer.exe command-line tool you can look for the installed versions of the Common Language Runtime. No CLR v3.0 yet ...