I don't use Empathy, but try this. Install Skype for Pidgin plugin from the Ubuntu Software Center. Open Skype and log in, and add your Skype account to Empathy protocol named ‘bigbrownchunx-skype-dbus’ or Pidgin Accounts --> Skype DBUS . You will need to allow Empathy/Pidgin access to Skype. ^{Source:J.Sneddon}

This protocol plugin allows libpurple to communicate with Skype.
Applications using libpurple (Pidgin, Finch, Empathy/Telepathy, etc.)
can thus show your Skype contacts alongside those from other
protocols, and you can communicate with them using that application
instead of the Skype user interface.

This plugin communicates with the Skype application in the background
to perform its work, so it's necessary to have Skype installed and
running. This product uses the Skype API but is not endorsed,
certified or otherwise approved in any way by Skype. ^Source:USC

OR

Skype-Wrapper is a small third-party ‘plugin’ that integrates many of Skype’s features directly into the Ubuntu desktop. This includes support for Ubuntu’s Messaging Menu, notification system and Unity launcher. ^{Source:J.Sneddon}

To install, just press Ctrl+Alt+T on your keyboard to open Terminal. When it opens, run the command(s) below:

sudo add-apt-repository ppa:skype-wrapper/ppa

sudo apt-get update

sudo apt-get install skype-wrapper python-skype