Thanks for the info on how Firefox does it. That's a bit more like the solution Peter Hosey proposed for Adium (see link in article). In that case, the alert is brought up front but not made key, meaning it won't accept key presses until you click on the window.

In the case I'm describing, it is not critical to have the alert come up immediately and having any sort of alert/dock icon bounce would be a distraction. In the cases I'm using it for now, it's for alerts that are the result of some timer so from the user's perspective, they can pop up at any time. The alert happens asynchronous to their flow of events so it can be disruptive if it happens while they are actively doing something.

But yes, for more critical/immediate alerts, something like what you or Peter described would be more appropriate.