Framework 3.5 is still working on CLR 2.0. V3 and V3.5 only added some (in fact) new classes, but did not change existing assemblies. The compiler has also changed, but in fact it is not runtime.
This is why in %windir%\Microsoft.NET\Framework\v3.5 (or Framwork64) you won’t find the assemblies already available in V2.
Framework V4 introduces a new version of the CLR. Accordingly, you will find all assemblies in %windir%\Microsoft.NET\Framework\v4.0.30319 .
The Versions and Dependencies page lists all versions, both the base class library version and the clr version.
[Edit] As soon as V4.5 is available soon, the same table will be available for the next version.
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