Comment 9 for bug 748516

The previous post helped me a bit but didn't solve the problem with disappearing eclipse.

So i've done a file /usr/share/applications/eclipse.desktop:

[Desktop Entry]
Name=Eclipse dev IDE
GenericName=Dev IDE
Comment=Write code in almost any language
Exec=gksu --description /usr/share/applications/eclipse.desktop /media/stor/dev/eclipse/eclipse.sh
Icon=/media/stor/dev/eclipse/icon.xpm
Terminal=false
Type=Application
Categories=Programming
NotShowIn=KDE;
X-Ubuntu-Gettext-Domain=eclipse

Take into account that I launch eclipse under root account - you may not need "gksu" if you want eclipse to run under you account.
And for sure you'll have to correct paths to match your eclipse install