You can replace the background image for the launchers with a transparent one. In a terminal, run the following (this is for Ubuntu 12.04, in 11.10 you'd change the path to say 4 instead of 5. For ubuntu 14.04 see the comments below):

1. Backup the original:

   
   
   

   sudo cp /usr/share/unity/5/launcher_icon_back_150.png{,.back}
   
   




2. Edit the file:

   
   
   

   gimp /usr/share/unity/5/launcher_icon_back_150.png
   
   




3. In GIMP, press Ctrl+A to select everything. Then Del to remove it. Hit Shift+Ctrl+S to save it as a new picture to, e.g., /home/launcher_icon_back_150.png, and finally press Ctrl+Q to quit.




4. Move the new image to the right place:

   
   
   

   sudo mv /home/launcher_icon_back_150.png /usr/share/unity/5/
   
   




5. Log out and back in.




6. If you want to go back, simply run:

   
   
   

   sudo mv /usr/share/unity/5/launcher_icon_back_150.png{.back,}
   
   

   
   
   

   and log out and back in again.