Note that the documentation for showMessage() states that messages are not guaranteed to be displayed. As a result, we have received a few requests for an API to query the position of the tray icon (and hence make it possible to popup custom balloons). The awesome news is that for Qt 4.3, we have added QSystemTrayIcon::geometry() that will return the geometry of the icon in global coordinates.
Oh and in case you missed Lars' post, Qt 4.3 snapshots are available here. We had to put in a few hacks to get geometry() to work reliably on all platforms. Let us know if it doesn't :)