The launcher icon overlays such as borders and highlights can be removed quite easily by changing 4 icon overlays in Unity.
1) Make a backup of the following image files in the folder
/usr/share/unity/4/
launcher_icon_back_54.png
launcher_icon_edge_54.png
launcher_icon_glow_62.png
launcher_icon_shine_54.png
2) Either make your own transparent images of the same size or download and unzip this file
http://ubuntuone.com/0CvxhLSPBpdxcAZ95FGoII
(from omgubuntu :)
3) replace those 4 files with the same 4 files downloaded from the above link
4) restart unity by pressing Alt+F2 and typing setsid unity (or logging out and in again)
5) if you don't like it then just replace the icons with the backed up icons and restart unity.
Example:
