Comment 5 for bug 480030

To get pidgin in the list, remove it from the blacklisted applications folder:

$ cd ~/.config/indicators/messages/applications-blacklist
$ mkdir ../un-blacklisted
$ mv pidgin-libnotify ../un-blacklisted/

Unfortunately, starting empathy puts it back in the blacklist, I simply removed empathy from the indicator applet:

$ cd /usr/share/indicators/messages/applications/
$ sudo mkdir ../../../old-indicators
$ sudo mv empathy ../../../old-indicators

After you close empathy, it should disappear from the indicator applet and pidgin should remain.

Hope it helps!~