I found a way to make the icon backgrounds transparent for the Unity Launcher by changing the files under /usr/share/unity/4.
Does anyone know how to make the background transparent for the launcher itself? I already made it transparent under Compiz, but I want to remove the line that separates the launcher from the desktop. If anything, I just want to make it look like the icons are floating.
You want to remove the 1px white border around the launcher, right? If that's the case, I believe it's hard coded and it's not something that can be achieved without messing up with unity source code, or in your case - with the unity-rotated one :)