Yeah, that's why I've used Pidgin more than Empathy. But the system tray icon just gets stashed in the messaging area, which isn't visible on the screen. And since there's no application list at the bottom GNOME 2 / Windows style, you don't see a flashing window or something when there's a message waiting. You still have to flip to the window, or open the messaging area to check if there are any messages that might be waiting if you didn't catch them when they came in. =\