I did the following:
gsettings set com.canonical.Unity.Panel systray-whitelist "['JavaEmbeddedFrame', 'Mumble', 'Wine', 'Skype', 'hp-systray', 'scp-dbus-service', 'Pidgin']"
and my skype and pidgin are shown on the systray. Now, i can find my skype.. Lets see how long it lasts... :)
Note: In pidgin the show in systray was marked as never i made it as always after the above step.