I have two web applications, one running under .Net 3.5, the other has been upgraded to .Net 4.0. Prior to the upgrade, shared authentication was setup and working correctly between the two applications as indicated in the MSDN article:
http://msdn.microsoft.com/en-us/library/eb0zx8fc.aspx
The 3.5 Application is running under the Classic .NET AppPool (v2.0, Classic Pipeline).
The 4.0 application is running under the ASP .NET v4.0 AppPool (v4.0, Integrated Pipeline).