Fluid, a site-specific browser generator for Mac, exposes a JavaScript Growl notification API [1]:
window.fluid.showGrowlNotification({
title: "title",
description: "description",
priority: 1,
sticky: false,
identifier: "foo",
onclick: callbackFunc,
icon: imgEl // or URL string
})
Relevant source is on the Fluid Developer page.
You can search for real-world examples at userscripts.org.
One downside with this approach is, of course, you have to force your users to use a Fluid browser when accessing the intranet application.
Setting up a bridge like Adam suggests has the advantage of requiring minimum effort from the users.