We don't use Zimbra Desktop (because it's an absolute beast of a program) but do use Zimbra in Firefox Prism WebApps.
That way it's completely isolated from other Firefox windows and has its own entries in the taskbar etc.
I've been longing to find a way to associate the mailto: handler with a Zimbra Prism webapp... as stated in my sig

But as yet I've been unable to solve this.
The ideal situation would be for there to be some sort of
lite client application that comes with Zimbra to register/preserve the mailto handler... basically like the old toaster.
However we're getting problems now since Prism is no longer being developed and is not supported by FF4.
Someone, somewhere really needs to come up with a new method for creating/creating standalone WebApps.
Be really great if all the settings for the WebApp could be provisioned from an XML file over HTTP. So if you need to change the Zimbra host/port (or the annoying webapp.ini/prefs.
js settings in Prism,) it could all be done remotely.
Chrome/Iron have an option in the menus to create a WebApp but all HTTP(S) links then open in a new Chrome/Iron window rather than in your default browser.