I read the article titled Using the .NET fusion API to manipulate the GAC yesterday. That article describes how to call fusion APIs from C++ code to programatically add assemblies to the global assembly cache (GAC) instead of using the .NET configuration utility or gacutil.exe.
In general, installing an assembly to the GAC is an application deployment activity, and is most often done during application setup. The article I read does not specifically say that C++ code should be used to install assemblies during application setup, but it does not say not to either. Therefore, I wanted to make sure that anyone reading this blog knows that you should not use C++ code or gacutil.exe to install assemblies during setup of your application.
You should use Windows Installer to install your application. Starting with version 2.0, Windows Installer has built-in functionality to install assemblies to the GAC - the MsiAssembly and MsiAssemblyName tables in particular. You can refer to this MSDN document for an overview of how to add assemblies to an MSI package and this MSDN document for a description of how to add Win32 assemblies to an MSI package. Therefore you should use this built-in functionality to handle GAC installation and uninstallation for you.
I would also like to point out that the Windows Vista Logo Program requirements document contains the following statement:
Gacutil must not be called from a custom action. Gacutil is not designed to be used during installation.
This means that if you want to obtain Windows Vista Logo certification for your application, you should use Windows Installer and the built-in GAC installation functionality for your setup.