Using javascript and AJAX, we have implemented a system that updates notifications for likes, subscribed threads, and PM's in the page title, similar to Facebook. We use it on our site:
http://psychopathfree.com/forum.php
It updates live, so even if they're visiting another site and the tab is sitting idle, they will see new notifications popup instantly.
It's not very good coding, and I'm sure there is a better way to do it

But if anyone would like this on their site, let me know. I would be happy to share our method.
In the past day alone of enabling it, we've seen a 400+% increase in user engagement, new posts, new activity, and online users.