Comment 0 for bug 1071914

1) do this of course:
gsettings set com.canonical.Unity.Panel systray-whitelist "['all']"
It allows to be visible all icons in Unity 2D system tray (in Unity 3D too of course).

2) remove packages:
indicator-messages
indicator-status-provider-pidgin
I don't want pidgin to be in ugly messages indicator.

3) default themes selected for all in pidgin, even smiles are disabled.

4) Gnome icon theme: Unity-icon-theme
GTK+ theme: Ambiance
Windows theme: Ambiance

5) Other applications icons showed good everywhere (desktop, folders, tray, menu).

6) In Unity 3D pidgin tray icon was invisible at first start but replaced to normal after 400ms.

7) Invisible icon of Pidgin is clickable and has context menu.

8) Maybe this helps:
http://askubuntu.com/questions/185612/pidgin-icon-not-showing-up-in-system-tray

ProblemType: Bug
DistroRelease: Ubuntu 12.04
Package: pidgin 1:2.10.3-0ubuntu1.1
Uname: Linux 3.5.7-zen-proxym-3 i686
ApportVersion: 2.0.1-0ubuntu14
Architecture: i386
Date: Sat Oct 27 00:57:53 2012
InstallationMedia: Ubuntu-Studio 10.10 "Maverick Meerkat" - Release i386 (20101008)
SourcePackage: pidgin
UpgradeStatus: Upgraded to precise on 2012-10-23 (3 days ago)