Why are there two icons in the Unity launcher for Nautilus?

According to the bug, you just need to remove the following line from your custom Nautilus launcher (~/.local/share/applications/nautilus-home.desktop):

OnlyShowIn=GNOME;Unity;

I had this problem and removing that line and logging out and logging back in worked for me.

Disclaimer: I am not a Linux programmer, and this answer contains modifying files out of your home folder. It works for me, but do it on your own risk.

This problem appears when you configure your Home icon to have a quicklist for your favourite places the way it is described here.

The way to solve it, as written on the Bug 842257 page, is instead of creating a copy of /usr/share/applications/nautilus-home.desktop in ~/.local/share/applications and modifying this copy, rather modifying the original file. So the steps are:

1. Delete the copy, if there is any: ~/.local/share/applications/nautilus-home.desktop

2. Open a terminal and write:

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

3. Add this text at the bottom of the file, save and close.

   X-Ayatana-Desktop-Shortcuts=Videos;Documents;Music;Pictures;Downloads
   [Videos Shortcut Group]
   Name=Videos
   Exec=nautilus Videos
   TargetEnvironment=Unity
   
   [Documents Shortcut Group]
   Name=Documents
   Exec=nautilus Documents
   TargetEnvironment=Unity
   
   [Music Shortcut Group]
   Name=Music
   Exec=nautilus Music
   TargetEnvironment=Unity
   
   [Pictures Shortcut Group]
   Name=Pictures
   Exec=nautilus Pictures
   TargetEnvironment=Unity
   
   [Downloads Shortcut Group]
   Name=Downloads
   Exec=nautilus Downloads
   TargetEnvironment=Unity
   

4. Reboot. It should work now, only one icon, with the quicklist.

If it still doesn't work, you can try Alt+F2, then run

unity --reset-icons

This will reset the icons of the original install on your launchbar, so you will have to repopulate it the way you want.

For getting the original nautilus-home.desktop file back, you can reinstall Nautilus and have the default settings and files:

sudo apt-get install --reinstall nautilus

This is a confirmed bug. Bug 842257

It will be fixed at some point. There should only be one icon in the Launcher.