Adding custom items to the panel – unity-2d

That was tricky!
There is no way to drag&drop push/pull/faceroll favorite app to launcher in unity-2d if you started it from terminal (or by other hacky way) except:
Read carefully the http://standards.freedesktop.org/desktop-entry-spec/latest/, or search for an existing .desktop files and modify that (#win):

akoskm@turing:~$ dpkg-query -S nautilus-home.desktop
nautilus: /usr/share/applications/nautilus-home.desktop

Now you know the location, let’s go and delete unnecessary things and modify patches according to your application:

gksu gedit /usr/share/applications/nautilus-home.desktop &

then File > Save As with the name of your application (I did this for eclipse so it will be eclipse-indigo.desktop).
Finally here is how my eclipse-indigo.desktop launcher looks like:

[Desktop Entry]
Version=1.0
Name=Eclipse Indigo
GenericName=IDE
Exec=/home/akoskm/Applications/eclipse-indigo/eclipse %U
Terminal=false
Icon=/home/akoskm/Applications/eclipse-indigo/icon.xpm
Type=Application
Categories=Programming;IDE;

Finally you should add it to the launcher. Start gconf-editor then navigate to /desktop/unity-2d/launcher.
Right-click to favorites key, Edit Key, Add and as New list value type the name of previously created .desktop file. Okay. You can move up/down the entries as you discovered already.
Now restart the panel:

killall unity-2d-launcher
.
You should see a launcher for your app.

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