InstallAware

Is there an easy (visual?) way to allow the user to control whether a shortcut appears on the desktop, in the quick launch and/or start menu?

Sure, but I'm afraid you can't do this using InstallAware's visual view just yet

You will probably want to add check boxes or radio buttons to your startmenu dialog. Then, set those fields to a script variable, and before calling the dialog, assign default values to those variables, representing how you initially wish the dialog to be configured. Finally, after the dialog has been called, test each variable and call the Create Shortcut command for the appropriate locations only if the corresponding variable is set to TRUE.

Of course, you may use the visual view to create the Create Shortcut commands that will actually create the shortcuts in your desired locations, just remember to switch to the code view after that, and wrap those commands inside IF blocks that test the variables returned from the startmenu dialog.