I have updated a quite old but useful article (Feb 2005) to document the new /ResetAddin command-line flag of Visual Studio 2005/2008 and how to do it correctly:

HOWTO: Removing commands and UI elements during Visual Studio .NET add-in uninstallation
http://www.mztools.com/articles/2005/MZ2005002.aspx

It is important to note that the /ResetAddin command-line flag will remove permanent controls but not permanent commandbars (another reason to not use them).