Today, I was installing SQL Server 2008 on a Windows Server 2008 R2 server. The setup detected that .NET 3.5 was missing and asked me to install this prerequisite. But after clicking OK, the setup prompted an error message of "You must use the Role Management Tool to install or configure Microsoft .NET Framework 3.5".
It seems like Windows 2008 R2 already ships with the .NET 3.5.1 framework so you just need to enable the feature from Server Manager. Afterwards it worked like a charm.