So much like with Facebook, if the chat window is updated and you don't currently have it on screen then the browsers taskbar icon will flash.
It would be nice if similar functionality could be added. Found some examples on stackoverflow just to make sure it was at all possible.
We have implemented the functionality for this to occur, but in most recent browsers they no longer flash unless there is an alert box which requires user input. In this case it would be deemed as annoying to the user to have an alert window to action every time they got a new message and the window was minimized. We have done the next best thing and the tab/window will change its title to notify you that there is a new message until it has been clicked on.
We hope that when HTML5 standards become more widespread we can possibly use the notify api within it to give a desktop notification of a new message coming in, although that also may become annoying to users so we will leave it for now and re-visit it later.
This will be put into the next version, good idea.