So I had successfully created a .desktop file to launch Eclipse from Gnome. I also found it no problem making it a favorite. The problem I was having was every time I launched Eclipse I ended up with 2 icons. The Favorite and one for the running process. The trick to making not getting this is to make sure the .desktop name matches the xwindows WM_CLASS property. You can get this value by running:
xprop WM_CLASS
Next click on the window of the Java application you are interested in. In the case of Eclipse the value is "Eclipse" so the file needs to be named Eclipse.desktop.
