This is NOT a request for killing applications.
I can well kill all process, no matter what. That's not the issue.
The issue is:
When we "close" Skype or Banshee, or Korganizer or many many others, it is common that, after we do that, **we have an icon on the panel (near the clock).
However, that has not been the case here.
Once I do that, I have no icon on the panel, near the clock, as a result, I can't easily re-display the application window as normally should happen.
How can make those icons appear on the panel ?
Do you have your "Notification Area Applet" in your panel? that's the place where all the applications goes when minimized to tray or closed while running (as in the case of banshee, rhythmbox and many more).
I would also suggest you to have the "Indicator Applet" http://launchpad.net/indicator-applet in order to have a different tray for having useful applications at the reach of a clic.
This applets can be added to your panel, by right clicking on it and choose "Add to Panel", then simply identify those applets that you need, and drag them to the panel.
Give this a chance and please let us know if this helps.
First install the package wmctrl
Then open a Terminal and run.
That should make the window visible. If it doesn't work run
look for a matchinhg window title and replace skype in the first command with the window title
Run the command
ps -aux
in a terminal and you will see a list all the open processes your machine is running. The second column indicates the PID of each process, and you can kill any process usingkill [PID]