How about being able to minimize ANY application and dragging it to the system tray. This way you wont have to wait for each app to implement this, reduce code bloat, and the rest of us wont have to wonder:
* Why isn't this app in the taskbar?
* What does close window do for this app?
* What does minimize do for this app?
* What does file quit do?
Nice idea. The top-right icons (at least, in XP) could be (from right to left): x to close, window to maximise, line to minimise to taskbar, and a dot (in a square) to minimise to the system tray.
Applications could then act differently based on where they were minimised - e.g., icon animations to convey a message, can't steal window focus, can show little alerts/messages, etc.
KDE allows this on a per application or per window basis "skip taskbar" and "skip pager". Sadly I don't think you can have alt-tab overlook such skipped pages.
