Version: (using Devel) Installed from: Compiled sources OS: Linux System tray icons and sys tray icon popups look very old fashioned; they're actually hard to get right on any platform. I think they're just plain old wrong. The best solution for KDE4 would have been if system tray icons were an integrated part of plasma. Not so square and popup-like as before, but smooth and animated, and appealing. We can change Qt to accommodate sexy system trays in Plasma. It would be just another one of those features that people love (as opposed to today, where it's mostly square, alien-looking and often misplaced.
The system tray follows the FDO spec. Applications are free to integrate directly with plasma in other ways (assuming missing that functionality on non KDE4 desktops isn't a problem) but the FDO spec is what it is.
I'm not familiar with the text of the FDO spec but I would like to see differentiation between the system tray icons and the quick launch icons other than their location. You could make the argument that this is a theme issue, but I think this should come top-down from KDE. For example iphone, mac osx, & openmoko all use B&W/grayscale system tray icons to differentiate a launcher from a running system tray process.