Copying the comments I wronly wrote on another bug:

Upstream does not suffer of this regression. It is introduced
in introduced by Ubuntu in debian/patches/30_raise_not_toggle.patch

It seems this bug was introduced on purpose (see #392153), which is a
shame.

In order to get the same behavior of empathy(upstream), you can do the
following:

$ sudo apt-get build-dep empathy
$ apt-get source empathy
$ cd empathy
$ rm debian/patches/30_raise_not_toggle.patch
$ dpkg-buildpackage -rfakeroot -b
$ cd ..
$ sudo dpkg -i empathy_2.28.0.*.deb

A change on this behaviour will not be accepted on the stable upstream.

** This bug is no longer a duplicate of bug 410278
   [Feature request]Allow empathy conversation window to be minimized to 
notification area or messaging menu

-- 
[karmic] Empathy don't close with click on notification area icon
https://bugs.launchpad.net/bugs/451568
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