One of the recurring discussions I seem to have with customers lately is "Why doesn't ClickOnce do..."  It is important to understand that ClickOnce was designed for a specific set of scenarios and is not intended to be a replacement for Windows Installer.  The MSDN article Choosing Between ClickOnce and Windows Installer does a great job of explaining this.  If you have asked yourself what the best way to deploy your Windows Forms 2.0 applications, then this is the article for you.