A Visual Studio Setup and Deployment project can be used to create a .msi installer the conditionally deploys different files based on the Intel processor architecture at runtime (when the installer runs).
The Condition property may be set for each file added to the Setup and Deployment project. To set the condition so that a file only installs on x64 computers, set the Condition property to "Intel=9" (without the quotes). To only install a file on win32 systems, set the Condition property to "Intel=0".
Important Update (17-Dec-2010) The above deployment suggestion for setting a launch condition to Intel=9 or Intel=0 no longer works (in more recent versions of Visual Studio since this original post). It does work however if you set the condition to "VersionNT64" and "NOT VersionNT64".