I have been using Gnome Shell but recently tried working with Unity in 12.04. I have a couple of oddball apps whose tray icons don't work well regardless of theme (they must be missing transparency). Two apps Yammer and Jungledisk are the problem. If I can find the actual icons I could probably fix them. The icons in /usr/share/pixmaps don't match what I see in the tray. See the two icons right next to Skype.