I never figured out how to do what your asking with Debian Gnome but this works just as well if not better for me.
Make a .desktop file in ~/.local/share/applications with the following content, edited for your setup of course. This will add it to the "start menu" or whatever one wants to call it. Just like any installed app. A logout / log in may be required to get it to register as an installed application.
Exec=java -jar /path/to/minecraft/jar/file
For icon I just found one using a google search of Minecraft icons.