A little while ago, I posted an introduction to a new .NET Framework Repair Tool that can be used to diagnose and repair .NET Framework 4 setup issues. An updated version of the repair tool has been released today to add support for diagnosing and repairing issues with .NET Framework 2.0 SP2, 3.0 SP2 and 3.5 SP1 setup. The repair tool can identify and fix issues with the installation of MSI-based versions of the .NET Framework, but it cannot fix issues related to versions of the .NET Framework that are installed as a part of Windows.
If you run into installation issues with the MSI-based versions of the .NET Framework 2.0 SP2, 3.0 SP2, 3.5 SP1 or 4, I strongly encourage you to download the .NET Framework Repair Tool and run it to see if it resolves your issue before resorting to trying the .NET Framework cleanup tool. Here are links that you can use to find additional information about the .NET Framework Repair Tool: