The following bug report in Unity makes it seem that Eclipse has been blacklisted from Unity’s global appmenu: https://bugs.launchpad.net/ubuntu/+source/eclipse/+bug/937965
I wanted this done to reclaim some real-estate on my screen. The blacklist has been hard-coded in the binary and we need to replace the contents in order to work around it.
> cd /usr/lib/x86_64-linux-gnu/gtk-2.0/2.10.0/menuproxies > sudo sed -i 's/Eclipse/Xclipse/' libappmenu.so
This works great, however I’ll suggest taking a backup of libappmenu.so before changing it. Good luck!