With Whidbey the directory structure of the global assembly cache changed. Using the Alpha version of Whidbey I cannot see the shared assemblies by opening the explorer to look at <windir>\assembly (using Windows XP). Of course it is possible to use the .NET 2.0 Framework Configuration utility to display these assemblies.
The reason for this is that the directory structure changed. The 1.0/1.1 shared assemblies are in the directory <windir>\assembly\GAC. The .NET 2.0 command line utility gacutil installs the shared assemblies into the directory <windir>\assembly\GAC_Neutral. Besides the directory GAC_Neutral there is a directory GAC_32 that keeps custom marshaler and Microsoft.VisualC assemblies.
I think the reason for this is the 64 bit version of .NET. Specific 64-bit assemblies (marshaling) will be in the GAC_64 directory, and the GAC_Neutral directory is for assemblies that are the same for both 32 and 64 bit versions.
This is a great feature of .NET: moving to 64 bit no changes are needed!
I remember a lot of hard work moving 16-bit applications to 32 bit!
Update: with the March Community Preview the directory GAC_Neutral changed to GAC_MSIL.