Use system-provided message/notification/pop-up APIs when available.
Under gnome/kde, this is the Desktop Notification spec <http://www.galago-project.org/specs/notification/0.9/index.html>, with high-level wrapper libnotify.
IIRC, Windows Vista will also have such a mechanism.
Adding support for this vastly simplifies code, improves desktop integration, and removes the possibility of pop-up related bugs on supported platforms.
I've modified my version (provided by Ubuntu) to handle this using pynotify.
care to share?