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Pidgin uses the Ubuntu Messaging Menu but many people prefer its old tray icon, which you could whitelist to use the systray. 

That's no longer possible out of the box with Ubuntu 13.04 and 13.10 because the Unity systray whitelist was removed (there is a PPA that restores the systray whitelist though) but luckily, Philip Langdale has created a plugin for Pidgin that provides an Ubuntu AppIndicator.

Pidgin Indicator Ubuntu

"I've found this indicator [Messaging Menu] to be much less usable than the original Pidgin tray icon, so I decided to build this plugin to restore the icon's functionality in a maintainable way (in constrat to having to run a patched version of Unity)."

- app description @ GitHub

Pidgin Indicator provides the same functionality as the original tray icon but a bit differently. For instance, to show the buddy list or unread messages you must middle click instead of left click (because left and right click on an AppIndicator do the same thing).

There is one small bug, but it shouldn't affect too many users: the Plugin Action menu items are not refreshed and you must restart Pidgin or reload the plugin to update these menu items. Hopefully this will be fixed in a future release.

Because there were no deb packages for Pidgin Indicator, I've uploaded it to the main WebUpd8 PPA, for Ubuntu 14.10, 14.04, 13.10, 13.04, 12.10 and 12.04, so you can install it easily.

Install Pidgin Indicator plugin in Ubuntu

To install Pidgin Indicator plugin in Ubuntu, use the following commands:
sudo add-apt-repository ppa:nilarimogard/webupd8
sudo apt-get update
sudo apt-get install pidgin-indicator
If you don't want to add the main WebUpd8 PPA, you can download the Pidgin Indicator deb from HERE and install it manually.

Once installed, open Pidgin and from its menu select Tools > Plugins, then scroll down until you see a plugin called "Ubuntu Indicator" and enable this plugin:

Pidgin Indicator plugin

That's it, Pidgin should now use an Ubuntu AppIndicator.

For source code, bug reports, etc., see the Pidgin Indicator GitHub page.