I am not sure exactly how to ask this question as I am not sure of the terminology I should use. I am writing a web application that is essentially a browser based IRC client. I wish to replicate some functionality I see in clients like x-chat where when you get a personal message it will alert the window manager. In my window manager (Aweosme wm) it turns the program tab red, in windows I imagine it would cause the programs button on the task bar to blink.
Essentially it's a notification that tells the window manager that something has happened and the program wants your attention.
You can't really make your browser window blink in the task bar. For HTML5 a Notification API was planned and so far Chrome supports it, but it seems that it was dropped again.
The only cross-browser possibilities to get the attention of your users are either to set the focus of the window:
window.focus();
or to change the title of your page:
document.title = "New message!";
See also this SO answer for a nice "blinky" implementation of changing document.title
.