.NET has defined a very solid convention for version numbers: major.minor.build.revision. Major version increments indicate structural changes; minor version changes indicate breaking changes. .NET 3.0 is neither a major or minor version change – it’s not even the same product.
Jason Zander addresses some of these concerns from the Microsoft perspective in detail on his blog, noting that the team has always thought of WinFX as being the same thing as the .NET Framework. Jason also elaborates in a Channel 9 video interview that the .NET Framework 3.0 will install both a 2.0 CLR and a 3.0 folder in the Microsoft .NET framework directory. Also, LINQ will be incluced in approximately .NET Framework 3.5 (version number again subject to change), but it does not require changes to the CLR itself, which is why the LINQ CTP can run against the 2.0 version of the CLR.