After installing Skype in your system , you may need to have it in tray icons or in message applications.
So for adding it in message applications first of all try to find ".desktop" file.
# locate skype.desktop
It will show you something like this:
Ok , now we get list of all message applications:
$ gsettings get com.canonical.indicator.messages applications
In my system , it returned me : "['pidgin.desktop']" . because I installed pidgin.
It maybe returns you different values because you may installed other message applications.
Ok , you we need to add "skype.desktop" in that list:
$ gsettings set com.canonical.indicator.messages applications "['pidgin.desktop','skype.desktop']"
Note: be careful you should add all of values + "skype.desktop" like I did above. I had "pidgin.desktop" + new application "skype.dekstop"