I was under the impression that the main .NET Assemblies are unchanged for .NET 3.0 and merely have the additional Assemblies for WPF, WCF, WWF and WCS. So .NET 3.0 is actually still based on the .NET 2.0 Common Runtime and so I would not expect the Base Class, CLR and Windows Forms Assembly versions to change - but that is a supposition on my part.
For .NET 3.5 I believe that it is still based on the .NET 2.0 CLR but that some fixes are made to the .NET 2.0 Assemblies which presumably will alter the Assembly version numbers.