The tray is nowhere near configurable enough, and in many cases it relies on the app being polite enough to stay the hell out when you tell it to (many apps are not, in my experience). Notifications from the tray are the real bitch. When watching movies on the HTPC I built with Vista, it frequently interrupts the movie to tell me vitally important information like, "I'm going to check for new Logitech upgrades now!" "No upgrades available." Java does it, too. Infuriating.

Maybe there is a way to disable this crap, but I've been unable to figure it out. (But I can't work iTunes, either, so I could just be stupid.)