the system tray on windows is the annoyance that it is for one huge reason: There is no other (decent) way to have a windowless app that can be interacted with. Because, there is no application list (aside from ctrl+alt+delete). I really think that Windows needs to move beyond windows as the highest level of organisation and allow the user to work with apps directly. I cannot see myself willingly using Windows until this is the case.

OSX for example: The dock is said list, and it performs the bulk of what the system tray ends up doing. the menu bar utilities on OS X perform what the system tray was intended to do.