One thing that Linux (well, my Gnome on Ubuntu 8.04), Mac, and Windows all fail at MISERABLY is the whole popping open unexpected windows thing.
Really, really, really, no window manager should EVER put another window in front of me while I'm doing something unrelated. Put it behind my current window. Put a notice on the task bar. Maybe even slide out a little notice bubble in the corner, but DON'T COVER WHAT I'M DOING, and DON'T STEAL MY KEYBOARD FOCUS!
I bet enough information is already available to most window managers to cover 95% of the cases where I currently have problems. Just come on folks, don't you think you can take care of this problem????