System tray icons disappeared after upgrading Ubuntu

You may need to do two things:

1. Install the sni-qt libraries.

Install sni-qt (click on the link), or with sudo apt-get install sni-qt sni-qt:i386 from the terminal, and then restart Skype. The tray/panel icon should now be back!

The reason this step is required is because sni-qt is installed automatically by the Ubuntu repository Skype package, but NOT by the Skype deb you directly download. Once Skype 4.0 is in the Ubuntu repos, you can install from there and this will no longer be necessary.

2. You may also need to whitelist the indicator

We don't know why, but for some systems this additional step is required before the indicator will show (thanks to Bruno Pereira!)

Steps:

1. Install the package dconf-tools (click on the link), or from the terminal with sudo apt-get install dconf-tools

2. Open dconf editor from the Dash (or dconf-editor from terminal):

   

3. On the left sidebar, use the triangles to navigate to desktop > unity > panel. On Ubuntu 12.10 you instead need to navigate to com > canonical > unity > panel. Double-click on the orange [JavaEmbedded...] part on the right, and add ,'skype' to allow the Skype indicator to show, as below:

   

4. Press Enter, close dconf editor, logout and login -- your indicator should now be back!

To have Skype Tray Icon displayed in Ubuntu, install sni-qt package:

sudo apt-get install sni-qt:i386

Enable Skype Icon on Unity Notification Panel on Ubuntu 12.04 LTS

When you do a fresh install of Ubuntu 12.04 (Or any version with Unity for that matter), you install Skype and expect it to work as it used to. But if you close the main window - you soon notice that Skype icon is not being displayed in top panel.

To fix this you will need to run a few commands. So open up your terminal and run this:

gsettings get com.canonical.Unity.Panel systray-whitelist

You should get something like this:

['JavaEmbeddedFrame', 'Wine', 'Update-notifier']

Basically this means, that Skype is not whitelisted, thus is not allowed by default to display its tray icon. We need to fix this. Append 'Skype' to the list so that you have something like this:

['JavaEmbeddedFrame', 'Wine', 'Update-notifier', 'Skype']

Then wrap it with double quotes (”) and add gsettings set com.canonical.Unity.Panel systray-whitelist in front of it. At this point you should have something like this:

gsettings set com.canonical.Unity.Panel systray-whitelist "['JavaEmbeddedFrame', 'Wine', 'Update-notifier', 'Skype']"

Now just copy this to your Terminal and execute the command. Reboot afterwards. Now you should see the icon.

Source: Enable Skype icon on Unity notification panel on Ubuntu 12.04 LTS - Tautvidas Sipavičius